$stepwise.lda
$stepwise.lda$max.p
[1] 15

$stepwise.lda$errors
 [1] 0.08029197 0.03649635 0.02189781 0.02189781 0.02189781 0.02189781
 [7] 0.02919708 0.02919708 0.02919708 0.02189781 0.02189781 0.02919708
[13] 0.02919708 0.02919708 0.03649635

$stepwise.lda$confusion.table
   step              error added.var added.var.name CTL.CTL CTL.PHO PHO.CTL
1     1 0.0802919708029197         1        Pho4p.1      90       6       5
2     2 0.0364963503649635         8      Pho4p.t.2      92       4       1
3     3 0.0218978102189781        12        Met4p.3      93       3       0
4     4 0.0218978102189781         5      Pho4p.g.2      93       3       0
5     5 0.0218978102189781         6      Pho4p.g.3      93       3       0
6     6 0.0218978102189781         9      Pho4p.t.3      93       3       0
7     7 0.0291970802919708         2        Pho4p.2      93       3       1
8     8 0.0291970802919708         3        Pho4p.3      93       3       1
9     9 0.0291970802919708         4      Pho4p.g.1      92       4       0
10   10 0.0218978102189781        10        Met4p.1      93       3       0
11   11 0.0218978102189781        11        Met4p.2      93       3       0
12   12 0.0291970802919708         7      Pho4p.t.1      92       4       0
13   13 0.0291970802919708        14       Met31p.2      92       4       0
14   14 0.0291970802919708        15       Met31p.3      92       4       0
15   15 0.0364963503649635        13       Met31p.1      92       4       1
   PHO.PHO
1       36
2       40
3       41
4       41
5       41
6       41
7       40
8       40
9       41
10      41
11      41
12      41
13      41
14      41
15      40

$stepwise.lda$best.pda
$stepwise.lda$best.pda$class
  [1] PHO CTL PHO PHO PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL PHO CTL PHO PHO
 [19] CTL CTL CTL CTL CTL PHO CTL PHO PHO PHO CTL PHO CTL PHO PHO PHO CTL PHO
 [37] CTL PHO PHO CTL CTL PHO PHO PHO CTL PHO CTL CTL CTL PHO CTL CTL CTL PHO
 [55] CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL PHO PHO CTL PHO PHO
 [73] CTL PHO CTL CTL PHO PHO CTL PHO CTL PHO PHO CTL CTL CTL CTL CTL CTL CTL
 [91] CTL CTL CTL CTL PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[109] PHO PHO CTL CTL CTL PHO PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[127] CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL
Levels: CTL PHO

$stepwise.lda$best.pda$posterior
                   CTL          PHO
YAL002W   1.506242e-04 9.998494e-01
YAL038W   5.551723e-01 4.448277e-01
YAR064W   1.271297e-01 8.728703e-01
YAR070C   1.522970e-06 9.999985e-01
YAR071W   2.777995e-05 9.999722e-01
YBL005W   9.999998e-01 1.546764e-07
YBL030C   9.999998e-01 1.984116e-07
YBR006W   9.999964e-01 3.626230e-06
YBR018C   9.999981e-01 1.853780e-06
YBR020W   9.999999e-01 1.188186e-07
YBR093C   7.023177e-06 9.999930e-01
YBR115C   1.000000e+00 1.780343e-08
YBR184W   9.999994e-01 6.471194e-07
YBR213W   9.997429e-01 2.571240e-04
YBR296C   5.671480e-08 9.999999e-01
YCL018W   9.999996e-01 3.706865e-07
YCR037C   5.951750e-06 9.999940e-01
YCR098C   1.102851e-05 9.999890e-01
YDL131W   9.999902e-01 9.831120e-06
YDL182W   9.999108e-01 8.924059e-05
YDL205C   1.000000e+00 2.264723e-08
YDL210W   9.999975e-01 2.537413e-06
YDR011W   9.999987e-01 1.258608e-06
YDR041W   3.723694e-04 9.996276e-01
YDR044W   9.999999e-01 5.328865e-08
YDR054C   2.612305e-03 9.973877e-01
YDR055W   1.018468e-02 9.898153e-01
YDR169C   6.463179e-07 9.999994e-01
YDR234W   9.999580e-01 4.195494e-05
YDR281C   6.198009e-05 9.999380e-01
YDR285W   1.000000e+00 8.249685e-09
YDR303C   4.527919e-04 9.995472e-01
YDR310C   1.448646e-05 9.999855e-01
YDR311W   5.457470e-05 9.999454e-01
YDR406W   9.999993e-01 6.999283e-07
YDR481C   8.219331e-02 9.178067e-01
YDR502C   9.999723e-01 2.769167e-05
YEL017C-A 3.811870e-06 9.999962e-01
YEL017W   1.057313e-04 9.998943e-01
YEL021W   1.000000e+00 1.726677e-08
YEL039C   1.000000e+00 9.142492e-09
YEL045C   1.582030e-04 9.998418e-01
YER017C   2.859619e-03 9.971404e-01
YER019W   2.859619e-03 9.971404e-01
YER026C   9.999811e-01 1.893593e-05
YER073W   3.302977e-05 9.999670e-01
YER086W   1.000000e+00 2.233340e-11
YER091C   9.975863e-01 2.413680e-03
YER179W   9.999988e-01 1.152721e-06
YFL004W   8.314857e-04 9.991685e-01
YFR030W   9.999782e-01 2.183416e-05
YGL009C   9.999997e-01 3.177705e-07
YGL073W   5.802530e-01 4.197470e-01
YGL213C   3.428698e-01 6.571302e-01
YGR019W   9.961807e-01 3.819342e-03
YGR044C   9.999624e-01 3.757954e-05
YGR088W   9.990258e-01 9.742112e-04
YGR121C   9.999987e-01 1.289954e-06
YGR157W   9.997526e-01 2.474144e-04
YGR233C   6.971758e-05 9.999303e-01
YGR281W   8.816792e-01 1.183208e-01
YHL022C   1.000000e+00 3.763913e-08
YHL036W   9.753687e-01 2.463128e-02
YHR007C   9.999848e-01 1.518460e-05
YHR008C   9.999964e-01 3.567893e-06
YHR014W   9.999839e-01 1.614164e-05
YHR037W   9.905608e-01 9.439187e-03
YHR136C   3.181701e-03 9.968183e-01
YHR137W   3.752834e-03 9.962472e-01
YHR153C   9.982200e-01 1.780039e-03
YHR168W   8.000158e-06 9.999920e-01
YHR215W   2.777995e-05 9.999722e-01
YIL015W   9.999997e-01 3.457058e-07
YIL046W   7.877299e-02 9.212270e-01
YIL072W   9.999989e-01 1.067725e-06
YIR017C   9.999089e-01 9.111768e-05
YIR034C   2.900579e-01 7.099421e-01
YJL012C   3.333943e-05 9.999667e-01
YJL106W   9.998403e-01 1.596682e-04
YJL117W   5.165371e-03 9.948346e-01
YJL153C   9.999993e-01 7.138324e-07
YJL209W   7.106385e-04 9.992894e-01
YJL211C   7.106385e-04 9.992894e-01
YJL219W   9.994824e-01 5.176157e-04
YJR010W   9.999971e-01 2.898142e-06
YJR048W   9.999961e-01 3.932023e-06
YJR073C   7.799600e-01 2.200400e-01
YJR094C   9.982089e-01 1.791065e-03
YJR137C   9.994802e-01 5.197642e-04
YJR152W   9.999906e-01 9.444124e-06
YKL001C   9.999287e-01 7.131304e-05
YKL182W   1.000000e+00 4.857313e-08
YKL216W   9.999986e-01 1.351431e-06
YKR039W   9.999999e-01 8.190101e-08
YKR048C   5.159267e-05 9.999484e-01
YKR050W   5.085099e-05 9.999491e-01
YKR069W   6.542622e-01 3.457378e-01
YLR081W   9.999991e-01 9.179681e-07
YLR142W   9.999949e-01 5.054355e-06
YLR180W   9.884996e-01 1.150036e-02
YLR263W   9.999999e-01 5.304204e-08
YLR303W   9.999799e-01 2.007904e-05
YLR329W   9.999330e-01 6.700772e-05
YLR420W   9.999452e-01 5.478303e-05
YLR438W   9.992641e-01 7.359329e-04
YML051W   9.999997e-01 2.546799e-07
YML054C   9.949565e-01 5.043465e-03
YML075C   9.999742e-01 2.583587e-05
YML121W   2.287485e-02 9.771252e-01
YML123C   3.641359e-11 1.000000e+00
YMR108W   9.999973e-01 2.690247e-06
YMR133W   1.000000e+00 3.801872e-10
YNL052W   9.999985e-01 1.494900e-06
YNL061W   1.239771e-05 9.999876e-01
YNL063W   1.315067e-03 9.986849e-01
YNL064C   3.312747e-04 9.996687e-01
YNL104C   9.025267e-01 9.747333e-02
YNL142W   1.000000e+00 2.810578e-08
YNL210W   9.999994e-01 5.927571e-07
YNL241C   9.998844e-01 1.156364e-04
YNL277W   9.999597e-01 4.029678e-05
YNR001C   9.999992e-01 7.973238e-07
YNR050C   9.934176e-01 6.582354e-03
YOL006C   9.998349e-01 1.651097e-04
YOR065W   9.956750e-01 4.324993e-03
YOR120W   9.999999e-01 1.096311e-07
YOR153W   9.997929e-01 2.071180e-04
YOR328W   9.999690e-01 3.100007e-05
YOR351C   1.000000e+00 2.095012e-09
YOR375C   9.998483e-01 1.517268e-04
YPL068C   1.053199e-02 9.894680e-01
YPL111W   9.999889e-01 1.110766e-05
YPL231W   9.723626e-01 2.763742e-02
YPR065W   9.999999e-01 1.095866e-07
YPR138C   9.999995e-01 4.801489e-07
YPR145W   9.996210e-01 3.789569e-04
YPR167C   9.999255e-01 7.445179e-05

$stepwise.lda$best.pda$call
lda(x = data.training, grouping = labels.training, CV = loo, 
    na.action = na.omit)

$stepwise.lda$best.pda$training.names
  [1] "YAL002W"   "YAL038W"   "YAR064W"   "YAR070C"   "YAR071W"   "YBL005W"  
  [7] "YBL030C"   "YBR006W"   "YBR018C"   "YBR020W"   "YBR093C"   "YBR115C"  
 [13] "YBR184W"   "YBR213W"   "YBR296C"   "YCL018W"   "YCR037C"   "YCR098C"  
 [19] "YDL131W"   "YDL182W"   "YDL205C"   "YDL210W"   "YDR011W"   "YDR041W"  
 [25] "YDR044W"   "YDR054C"   "YDR055W"   "YDR169C"   "YDR234W"   "YDR281C"  
 [31] "YDR285W"   "YDR303C"   "YDR310C"   "YDR311W"   "YDR406W"   "YDR481C"  
 [37] "YDR502C"   "YEL017C-A" "YEL017W"   "YEL021W"   "YEL039C"   "YEL045C"  
 [43] "YER017C"   "YER019W"   "YER026C"   "YER073W"   "YER086W"   "YER091C"  
 [49] "YER179W"   "YFL004W"   "YFR030W"   "YGL009C"   "YGL073W"   "YGL213C"  
 [55] "YGR019W"   "YGR044C"   "YGR088W"   "YGR121C"   "YGR157W"   "YGR233C"  
 [61] "YGR281W"   "YHL022C"   "YHL036W"   "YHR007C"   "YHR008C"   "YHR014W"  
 [67] "YHR037W"   "YHR136C"   "YHR137W"   "YHR153C"   "YHR168W"   "YHR215W"  
 [73] "YIL015W"   "YIL046W"   "YIL072W"   "YIR017C"   "YIR034C"   "YJL012C"  
 [79] "YJL106W"   "YJL117W"   "YJL153C"   "YJL209W"   "YJL211C"   "YJL219W"  
 [85] "YJR010W"   "YJR048W"   "YJR073C"   "YJR094C"   "YJR137C"   "YJR152W"  
 [91] "YKL001C"   "YKL182W"   "YKL216W"   "YKR039W"   "YKR048C"   "YKR050W"  
 [97] "YKR069W"   "YLR081W"   "YLR142W"   "YLR180W"   "YLR263W"   "YLR303W"  
[103] "YLR329W"   "YLR420W"   "YLR438W"   "YML051W"   "YML054C"   "YML075C"  
[109] "YML121W"   "YML123C"   "YMR108W"   "YMR133W"   "YNL052W"   "YNL061W"  
[115] "YNL063W"   "YNL064C"   "YNL104C"   "YNL142W"   "YNL210W"   "YNL241C"  
[121] "YNL277W"   "YNR001C"   "YNR050C"   "YOL006C"   "YOR065W"   "YOR120W"  
[127] "YOR153W"   "YOR328W"   "YOR351C"   "YOR375C"   "YPL068C"   "YPL111W"  
[133] "YPL231W"   "YPR065W"   "YPR138C"   "YPR145W"   "YPR167C"  

$stepwise.lda$best.pda$training.label
  [1] PHO CTL PHO PHO PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL PHO CTL PHO PHO
 [19] CTL CTL CTL CTL CTL PHO CTL PHO PHO PHO CTL PHO CTL PHO PHO PHO CTL PHO
 [37] CTL PHO PHO CTL CTL PHO PHO PHO CTL PHO CTL CTL CTL PHO CTL CTL CTL CTL
 [55] CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL PHO PHO CTL PHO PHO
 [73] CTL CTL CTL CTL CTL PHO CTL PHO CTL PHO PHO CTL CTL CTL CTL CTL CTL CTL
 [91] CTL CTL CTL CTL PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[109] PHO PHO CTL CTL CTL PHO PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[127] CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL
Levels: CTL PHO

$stepwise.lda$best.pda$pda.method
[1] "lda"

$stepwise.lda$best.pda$loo
[1] TRUE

$stepwise.lda$best.pda$validation
[1] "LOO"

$stepwise.lda$best.pda$confusion
      true
object CTL PHO
   CTL  93   0
   PHO   3  41
attr(,"error")
[1] 0.02189781


$stepwise.lda$best.p
[1] 11

$stepwise.lda$best.vars
 [1]  1  8 12  5  6  9  2  3  4 10 11

$stepwise.lda$best.var.names
 [1] "Pho4p.1"   "Pho4p.t.2" "Met4p.3"   "Pho4p.g.2" "Pho4p.g.3" "Pho4p.t.3"
 [7] "Pho4p.2"   "Pho4p.3"   "Pho4p.g.1" "Met4p.1"   "Met4p.2"  

$stepwise.lda$best.error
[1] 0.02189781

$stepwise.lda$pc.transform
[1] FALSE

$stepwise.lda$var.order
 [1]  1  8 12  5  6  9  2  3  4 10 11  7 14 15 13


$pc.stepwise.lda
$pc.stepwise.lda$max.p
[1] 15

$pc.stepwise.lda$errors
 [1] 0.13138686 0.08029197 0.05839416 0.04379562 0.01459854 0.01459854
 [7] 0.01459854 0.00729927 0.00729927 0.01459854 0.01459854 0.01459854
[13] 0.02189781 0.02919708 0.03649635

$pc.stepwise.lda$confusion.table
   step              error added.var added.var.name CTL.CTL CTL.PHO PHO.CTL
1     1  0.131386861313869         1         Comp.1      86      10       8
2     2 0.0802919708029197         5         Comp.5      88       8       3
3     3 0.0583941605839416         2         Comp.2      91       5       3
4     4 0.0437956204379562         3         Comp.3      91       5       1
5     5 0.0145985401459854         7         Comp.7      94       2       0
6     6 0.0145985401459854         9         Comp.9      94       2       0
7     7 0.0145985401459854        11        Comp.11      94       2       0
8     8 0.0072992700729927        15        Comp.15      95       1       0
9     9 0.0072992700729927        12        Comp.12      95       1       0
10   10 0.0145985401459854         6         Comp.6      94       2       0
11   11 0.0145985401459854        10        Comp.10      94       2       0
12   12 0.0145985401459854        14        Comp.14      94       2       0
13   13 0.0218978102189781        13        Comp.13      93       3       0
14   14 0.0291970802919708         8         Comp.8      93       3       1
15   15 0.0364963503649635         4         Comp.4      92       4       1
   PHO.PHO
1       33
2       38
3       38
4       40
5       41
6       41
7       41
8       41
9       41
10      41
11      41
12      41
13      41
14      40
15      40

$pc.stepwise.lda$best.pda
$pc.stepwise.lda$best.pda$class
  [1] PHO CTL PHO PHO PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL PHO CTL PHO PHO
 [19] CTL CTL CTL CTL CTL PHO CTL PHO PHO PHO CTL PHO CTL PHO PHO PHO CTL PHO
 [37] CTL PHO PHO CTL CTL PHO PHO PHO CTL PHO CTL CTL CTL PHO CTL CTL PHO CTL
 [55] CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL PHO PHO CTL PHO PHO
 [73] CTL CTL CTL CTL CTL PHO CTL PHO CTL PHO PHO CTL CTL CTL CTL CTL CTL CTL
 [91] CTL CTL CTL CTL PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[109] PHO PHO CTL CTL CTL PHO PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[127] CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL
Levels: CTL PHO

$pc.stepwise.lda$best.pda$posterior
                   CTL          PHO
YAL002W   1.180361e-03 9.988196e-01
YAL038W   8.543830e-01 1.456170e-01
YAR064W   3.071900e-01 6.928100e-01
YAR070C   2.994904e-06 9.999970e-01
YAR071W   7.387602e-06 9.999926e-01
YBL005W   9.999928e-01 7.235394e-06
YBL030C   9.999927e-01 7.281309e-06
YBR006W   9.999789e-01 2.114016e-05
YBR018C   9.999974e-01 2.644492e-06
YBR020W   9.999906e-01 9.406706e-06
YBR093C   3.191235e-06 9.999968e-01
YBR115C   9.999995e-01 5.315754e-07
YBR184W   9.999803e-01 1.965436e-05
YBR213W   9.999859e-01 1.408383e-05
YBR296C   2.156637e-07 9.999998e-01
YCL018W   9.999987e-01 1.312935e-06
YCR037C   6.959307e-03 9.930407e-01
YCR098C   1.662449e-04 9.998338e-01
YDL131W   9.995080e-01 4.919913e-04
YDL182W   9.792698e-01 2.073024e-02
YDL205C   9.999996e-01 3.943364e-07
YDL210W   9.999987e-01 1.345061e-06
YDR011W   9.999989e-01 1.077497e-06
YDR041W   1.461670e-03 9.985383e-01
YDR044W   9.999906e-01 9.442551e-06
YDR054C   4.078607e-03 9.959214e-01
YDR055W   1.387706e-02 9.861229e-01
YDR169C   1.182660e-06 9.999988e-01
YDR234W   9.999032e-01 9.678357e-05
YDR281C   2.878139e-04 9.997122e-01
YDR285W   9.999999e-01 1.024068e-07
YDR303C   9.250694e-03 9.907493e-01
YDR310C   6.596545e-04 9.993403e-01
YDR311W   7.962160e-04 9.992038e-01
YDR406W   9.999597e-01 4.031134e-05
YDR481C   3.825762e-01 6.174238e-01
YDR502C   9.999988e-01 1.172719e-06
YEL017C-A 1.278140e-04 9.998722e-01
YEL017W   1.420018e-03 9.985800e-01
YEL021W   9.999991e-01 9.083170e-07
YEL039C   9.999983e-01 1.650421e-06
YEL045C   4.102571e-03 9.958974e-01
YER017C   3.317710e-04 9.996682e-01
YER019W   6.553915e-04 9.993446e-01
YER026C   9.999415e-01 5.847682e-05
YER073W   3.055636e-04 9.996944e-01
YER086W   1.000000e+00 3.183466e-09
YER091C   9.975726e-01 2.427413e-03
YER179W   9.999996e-01 4.379567e-07
YFL004W   5.394447e-04 9.994606e-01
YFR030W   9.987494e-01 1.250570e-03
YGL009C   9.999999e-01 1.205600e-07
YGL073W   2.921445e-02 9.707855e-01
YGL213C   5.103417e-01 4.896583e-01
YGR019W   9.997126e-01 2.873944e-04
YGR044C   9.985419e-01 1.458125e-03
YGR088W   9.975697e-01 2.430290e-03
YGR121C   9.999727e-01 2.728126e-05
YGR157W   9.999966e-01 3.430057e-06
YGR233C   6.004864e-03 9.939951e-01
YGR281W   9.997374e-01 2.626383e-04
YHL022C   9.999999e-01 5.829156e-08
YHL036W   9.984125e-01 1.587525e-03
YHR007C   9.997785e-01 2.214538e-04
YHR008C   9.999339e-01 6.612861e-05
YHR014W   9.999787e-01 2.125697e-05
YHR037W   9.791076e-01 2.089245e-02
YHR136C   3.694645e-03 9.963054e-01
YHR137W   3.782415e-03 9.962176e-01
YHR153C   9.998465e-01 1.534510e-04
YHR168W   1.542028e-06 9.999985e-01
YHR215W   7.387602e-06 9.999926e-01
YIL015W   9.999990e-01 1.015342e-06
YIL046W   5.950197e-01 4.049803e-01
YIL072W   9.999984e-01 1.617301e-06
YIR017C   9.999567e-01 4.329454e-05
YIR034C   5.462245e-01 4.537755e-01
YJL012C   5.945531e-05 9.999405e-01
YJL106W   9.999049e-01 9.507339e-05
YJL117W   6.821693e-03 9.931783e-01
YJL153C   9.999944e-01 5.649777e-06
YJL209W   9.103897e-03 9.908961e-01
YJL211C   9.103897e-03 9.908961e-01
YJL219W   9.875009e-01 1.249908e-02
YJR010W   9.999977e-01 2.334443e-06
YJR048W   9.999720e-01 2.801035e-05
YJR073C   8.846898e-01 1.153102e-01
YJR094C   9.980539e-01 1.946055e-03
YJR137C   8.562330e-01 1.437670e-01
YJR152W   9.990810e-01 9.190066e-04
YKL001C   9.998944e-01 1.055984e-04
YKL182W   9.999984e-01 1.573320e-06
YKL216W   9.999868e-01 1.320916e-05
YKR039W   9.999997e-01 2.586475e-07
YKR048C   2.843099e-03 9.971569e-01
YKR050W   2.765633e-03 9.972344e-01
YKR069W   8.512199e-01 1.487801e-01
YLR081W   9.999603e-01 3.965565e-05
YLR142W   9.999720e-01 2.804877e-05
YLR180W   9.994980e-01 5.020017e-04
YLR263W   1.000000e+00 3.561829e-08
YLR303W   9.998574e-01 1.425710e-04
YLR329W   9.995704e-01 4.296344e-04
YLR420W   9.997158e-01 2.842057e-04
YLR438W   9.931149e-01 6.885124e-03
YML051W   9.999977e-01 2.251836e-06
YML054C   6.141926e-01 3.858074e-01
YML075C   9.999874e-01 1.264866e-05
YML121W   4.308572e-03 9.956914e-01
YML123C   1.804060e-12 1.000000e+00
YMR108W   9.992875e-01 7.124524e-04
YMR133W   1.000000e+00 1.161215e-08
YNL052W   9.999886e-01 1.143485e-05
YNL061W   2.985695e-03 9.970143e-01
YNL063W   1.804604e-03 9.981954e-01
YNL064C   7.825465e-04 9.992175e-01
YNL104C   8.791805e-01 1.208195e-01
YNL142W   9.999989e-01 1.053577e-06
YNL210W   9.999997e-01 2.613665e-07
YNL241C   9.999904e-01 9.583206e-06
YNL277W   9.995116e-01 4.883835e-04
YNR001C   9.999994e-01 5.839369e-07
YNR050C   9.811485e-01 1.885152e-02
YOL006C   9.997514e-01 2.486431e-04
YOR065W   9.360998e-01 6.390021e-02
YOR120W   9.999999e-01 6.369000e-08
YOR153W   9.996168e-01 3.831822e-04
YOR328W   9.998523e-01 1.477410e-04
YOR351C   9.999990e-01 1.009612e-06
YOR375C   9.992742e-01 7.258319e-04
YPL068C   4.415335e-04 9.995585e-01
YPL111W   9.999963e-01 3.684181e-06
YPL231W   9.950837e-01 4.916314e-03
YPR065W   9.999991e-01 9.464344e-07
YPR138C   9.999980e-01 1.992038e-06
YPR145W   9.878468e-01 1.215325e-02
YPR167C   9.999477e-01 5.232916e-05

$pc.stepwise.lda$best.pda$call
lda(x = data.training, grouping = labels.training, CV = loo, 
    na.action = na.omit)

$pc.stepwise.lda$best.pda$training.names
  [1] "YAL002W"   "YAL038W"   "YAR064W"   "YAR070C"   "YAR071W"   "YBL005W"  
  [7] "YBL030C"   "YBR006W"   "YBR018C"   "YBR020W"   "YBR093C"   "YBR115C"  
 [13] "YBR184W"   "YBR213W"   "YBR296C"   "YCL018W"   "YCR037C"   "YCR098C"  
 [19] "YDL131W"   "YDL182W"   "YDL205C"   "YDL210W"   "YDR011W"   "YDR041W"  
 [25] "YDR044W"   "YDR054C"   "YDR055W"   "YDR169C"   "YDR234W"   "YDR281C"  
 [31] "YDR285W"   "YDR303C"   "YDR310C"   "YDR311W"   "YDR406W"   "YDR481C"  
 [37] "YDR502C"   "YEL017C-A" "YEL017W"   "YEL021W"   "YEL039C"   "YEL045C"  
 [43] "YER017C"   "YER019W"   "YER026C"   "YER073W"   "YER086W"   "YER091C"  
 [49] "YER179W"   "YFL004W"   "YFR030W"   "YGL009C"   "YGL073W"   "YGL213C"  
 [55] "YGR019W"   "YGR044C"   "YGR088W"   "YGR121C"   "YGR157W"   "YGR233C"  
 [61] "YGR281W"   "YHL022C"   "YHL036W"   "YHR007C"   "YHR008C"   "YHR014W"  
 [67] "YHR037W"   "YHR136C"   "YHR137W"   "YHR153C"   "YHR168W"   "YHR215W"  
 [73] "YIL015W"   "YIL046W"   "YIL072W"   "YIR017C"   "YIR034C"   "YJL012C"  
 [79] "YJL106W"   "YJL117W"   "YJL153C"   "YJL209W"   "YJL211C"   "YJL219W"  
 [85] "YJR010W"   "YJR048W"   "YJR073C"   "YJR094C"   "YJR137C"   "YJR152W"  
 [91] "YKL001C"   "YKL182W"   "YKL216W"   "YKR039W"   "YKR048C"   "YKR050W"  
 [97] "YKR069W"   "YLR081W"   "YLR142W"   "YLR180W"   "YLR263W"   "YLR303W"  
[103] "YLR329W"   "YLR420W"   "YLR438W"   "YML051W"   "YML054C"   "YML075C"  
[109] "YML121W"   "YML123C"   "YMR108W"   "YMR133W"   "YNL052W"   "YNL061W"  
[115] "YNL063W"   "YNL064C"   "YNL104C"   "YNL142W"   "YNL210W"   "YNL241C"  
[121] "YNL277W"   "YNR001C"   "YNR050C"   "YOL006C"   "YOR065W"   "YOR120W"  
[127] "YOR153W"   "YOR328W"   "YOR351C"   "YOR375C"   "YPL068C"   "YPL111W"  
[133] "YPL231W"   "YPR065W"   "YPR138C"   "YPR145W"   "YPR167C"  

$pc.stepwise.lda$best.pda$training.label
  [1] PHO CTL PHO PHO PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL PHO CTL PHO PHO
 [19] CTL CTL CTL CTL CTL PHO CTL PHO PHO PHO CTL PHO CTL PHO PHO PHO CTL PHO
 [37] CTL PHO PHO CTL CTL PHO PHO PHO CTL PHO CTL CTL CTL PHO CTL CTL CTL CTL
 [55] CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL PHO PHO CTL PHO PHO
 [73] CTL CTL CTL CTL CTL PHO CTL PHO CTL PHO PHO CTL CTL CTL CTL CTL CTL CTL
 [91] CTL CTL CTL CTL PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[109] PHO PHO CTL CTL CTL PHO PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[127] CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL
Levels: CTL PHO

$pc.stepwise.lda$best.pda$pda.method
[1] "lda"

$pc.stepwise.lda$best.pda$loo
[1] TRUE

$pc.stepwise.lda$best.pda$validation
[1] "LOO"

$pc.stepwise.lda$best.pda$confusion
      true
object CTL PHO
   CTL  95   0
   PHO   1  41
attr(,"error")
[1] 0.00729927


$pc.stepwise.lda$best.p
[1] 9

$pc.stepwise.lda$best.vars
[1]  1  5  2  3  7  9 11 15 12

$pc.stepwise.lda$best.var.names
[1] "Comp.1"  "Comp.5"  "Comp.2"  "Comp.3"  "Comp.7"  "Comp.9"  "Comp.11"
[8] "Comp.15" "Comp.12"

$pc.stepwise.lda$best.error
[1] 0.00729927

$pc.stepwise.lda$pc.transform
[1] TRUE

$pc.stepwise.lda$var.order
 [1]  1  5  2  3  7  9 11 15 12  6 10 14 13  8  4


$permut.stepwise.lda
$permut.stepwise.lda$confusion.table
        error CTL.CTL CTL.PHO PHO.CTL PHO.PHO
1   0.2846715      96       0      39       2
2   0.2481752      91       5      29      12
3   0.2992701      96       0      41       0
4   0.2700730      92       4      33       8
5   0.2992701      89       7      34       7
6   0.2992701      96       0      41       0
7   0.2992701      96       0      41       0
8   0.2773723      94       2      36       5
9   0.2992701      96       0      41       0
10  0.2700730      89       7      30      11
11  0.2992701      91       5      36       5
12  0.2773723      91       5      33       8
13  0.2919708      96       0      40       1
14  0.2992701      96       0      41       0
15  0.2992701      93       3      38       3
16  0.2919708      93       3      37       4
17  0.2773723      95       1      37       4
18  0.2773723      92       4      34       7
19  0.2919708      96       0      40       1
20  0.2992701      96       0      41       0
21  0.2627737      93       3      33       8
22  0.2992701      96       0      41       0
23  0.2992701      96       0      41       0
24  0.2919708      95       1      39       2
25  0.2992701      96       0      41       0
26  0.2627737      93       3      33       8
27  0.2992701      95       1      40       1
28  0.2627737      88       8      28      13
29  0.2992701      96       0      41       0
30  0.2992701      95       1      40       1
31  0.2773723      96       0      38       3
32  0.2992701      96       0      41       0
33  0.2773723      94       2      36       5
34  0.2992701      96       0      41       0
35  0.2846715      92       4      35       6
36  0.2992701      94       2      39       2
37  0.2627737      94       2      34       7
38  0.2992701      96       0      41       0
39  0.2992701      96       0      41       0
40  0.2992701      96       0      41       0
41  0.2846715      94       2      37       4
42  0.2992701      96       0      41       0
43  0.2700730      90       6      31      10
44  0.2992701      96       0      41       0
45  0.2992701      96       0      41       0
46  0.2700730      95       1      36       5
47  0.2919708      89       7      33       8
48  0.2919708      89       7      33       8
49  0.2992701      94       2      39       2
50  0.2992701      96       0      41       0
51  0.2846715      93       3      36       5
52  0.2992701      92       4      37       4
53  0.2554745      93       3      32       9
54  0.2846715      96       0      39       2
55  0.2846715      89       7      32       9
56  0.2919708      95       1      39       2
57  0.2554745      90       6      29      12
58  0.2846715      93       3      36       5
59  0.2992701      95       1      40       1
60  0.2773723      93       3      35       6
61  0.2992701      96       0      41       0
62  0.2992701      96       0      41       0
63  0.2992701      96       0      41       0
64  0.2773723      91       5      33       8
65  0.2992701      96       0      41       0
66  0.2919708      95       1      39       2
67  0.2992701      91       5      36       5
68  0.2919708      96       0      40       1
69  0.2992701      96       0      41       0
70  0.2992701      96       0      41       0
71  0.2992701      96       0      41       0
72  0.2627737      89       7      29      12
73  0.2992701      96       0      41       0
74  0.2773723      90       6      32       9
75  0.2919708      96       0      40       1
76  0.2992701      90       6      35       6
77  0.2992701      96       0      41       0
78  0.2773723      91       5      33       8
79  0.2846715      96       0      39       2
80  0.2919708      94       2      38       3
81  0.2992701      89       7      34       7
82  0.2992701      92       4      37       4
83  0.2919708      96       0      40       1
84  0.2554745      90       6      29      12
85  0.2700730      94       2      35       6
86  0.2919708      90       6      34       7
87  0.2992701      96       0      41       0
88  0.2992701      85      11      30      11
89  0.2846715      92       4      35       6
90  0.2919708      95       1      39       2
91  0.2992701      96       0      41       0
92  0.2919708      95       1      39       2
93  0.2992701      96       0      41       0
94  0.2773723      90       6      32       9
95  0.2846715      96       0      39       2
96  0.2846715      95       1      38       3
97  0.2773723      94       2      36       5
98  0.2992701      96       0      41       0
99  0.2992701      95       1      40       1
100 0.2189781      93       3      27      14

$permut.stepwise.lda$errors
    permut.1  permut.2  permut.3  permut.4  permut.5  permut.6  permut.7
1  0.2992701 0.2919708 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
2  0.2846715 0.2700730 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
3  0.2846715 0.2481752 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
4  0.2919708 0.2481752 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
5  0.2992701 0.2481752 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
6  0.2992701 0.2554745 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
7  0.2992701 0.2627737 0.2992701 0.2773723 0.3065693 0.2992701 0.3065693
8  0.3065693 0.2627737 0.3065693 0.2773723 0.3065693 0.2992701 0.3065693
9  0.3065693 0.2627737 0.3138686 0.2773723 0.2992701 0.2992701 0.3065693
10 0.3138686 0.2627737 0.3065693 0.2700730 0.3065693 0.2992701 0.3138686
11 0.3211679 0.2773723 0.3138686 0.2700730 0.3065693 0.3065693 0.3284672
12 0.3138686 0.2773723 0.3211679 0.2846715 0.3065693 0.3138686 0.3284672
13 0.2919708 0.2773723 0.3284672 0.2992701 0.3065693 0.3357664 0.3357664
14 0.3430657 0.2919708 0.3430657 0.2919708 0.3065693 0.3503650 0.3357664
15 0.3430657 0.2919708 0.3722628 0.2992701 0.3503650 0.3722628 0.3357664
    permut.8  permut.9 permut.10 permut.11 permut.12 permut.13 permut.14
1  0.2919708 0.2992701 0.2773723 0.2992701 0.2992701 0.2992701 0.2992701
2  0.2846715 0.2992701 0.2846715 0.2992701 0.2992701 0.2992701 0.2992701
3  0.2773723 0.2992701 0.2846715 0.2992701 0.2773723 0.2992701 0.2992701
4  0.2773723 0.2992701 0.2773723 0.2992701 0.2773723 0.2919708 0.2992701
5  0.2773723 0.2992701 0.2846715 0.2992701 0.2773723 0.2919708 0.3065693
6  0.2773723 0.2992701 0.2919708 0.2992701 0.2773723 0.2919708 0.3211679
7  0.2846715 0.2992701 0.2846715 0.2992701 0.2773723 0.2919708 0.3138686
8  0.2992701 0.2992701 0.2700730 0.2992701 0.2919708 0.2992701 0.3138686
9  0.3138686 0.2992701 0.2846715 0.3065693 0.2992701 0.2992701 0.3211679
10 0.3138686 0.2992701 0.2773723 0.3065693 0.2992701 0.2992701 0.3357664
11 0.3284672 0.2992701 0.2773723 0.2992701 0.3065693 0.3138686 0.3430657
12 0.3430657 0.2992701 0.2846715 0.2992701 0.3138686 0.3138686 0.3503650
13 0.3503650 0.2992701 0.2992701 0.3065693 0.3138686 0.3430657 0.3357664
14 0.3503650 0.3138686 0.3211679 0.3065693 0.3211679 0.3503650 0.3503650
15 0.3430657 0.3430657 0.3138686 0.3357664 0.3284672 0.3649635 0.3722628
   permut.15 permut.16 permut.17 permut.18 permut.19 permut.20 permut.21
1  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2846715
2  0.2992701 0.2992701 0.2992701 0.2992701 0.2919708 0.2992701 0.2700730
3  0.2992701 0.2992701 0.2992701 0.2919708 0.2919708 0.2992701 0.2627737
4  0.2992701 0.2919708 0.2992701 0.2773723 0.2992701 0.2992701 0.2627737
5  0.2992701 0.2919708 0.2919708 0.2773723 0.2919708 0.2992701 0.2627737
6  0.2992701 0.2919708 0.2919708 0.2919708 0.2919708 0.2992701 0.2700730
7  0.2992701 0.2992701 0.2846715 0.2846715 0.2992701 0.2992701 0.2773723
8  0.2992701 0.2992701 0.2773723 0.2773723 0.3065693 0.3211679 0.2846715
9  0.2992701 0.3138686 0.2773723 0.2846715 0.3065693 0.3211679 0.2846715
10 0.3065693 0.3065693 0.2846715 0.2846715 0.3138686 0.3211679 0.2919708
11 0.3138686 0.3211679 0.2919708 0.3138686 0.3211679 0.3284672 0.3065693
12 0.3211679 0.3211679 0.3138686 0.3357664 0.3430657 0.3357664 0.3065693
13 0.3357664 0.3357664 0.3138686 0.3430657 0.3576642 0.3503650 0.3211679
14 0.3503650 0.3576642 0.3211679 0.3576642 0.3576642 0.3649635 0.3138686
15 0.3430657 0.3576642 0.3211679 0.3576642 0.3722628 0.3795620 0.3284672
   permut.22 permut.23 permut.24 permut.25 permut.26 permut.27 permut.28
1  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
2  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
3  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
4  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2919708
5  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2919708
6  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.3065693 0.3065693
7  0.2992701 0.3065693 0.2992701 0.2992701 0.2992701 0.2992701 0.2919708
8  0.2992701 0.3138686 0.2919708 0.2992701 0.2992701 0.3065693 0.2992701
9  0.2992701 0.3138686 0.2919708 0.2992701 0.2992701 0.2992701 0.3138686
10 0.2992701 0.3284672 0.2919708 0.3065693 0.2627737 0.2992701 0.2773723
11 0.2992701 0.3357664 0.2992701 0.3211679 0.2627737 0.3138686 0.2700730
12 0.2992701 0.3284672 0.3065693 0.3211679 0.2627737 0.3430657 0.2627737
13 0.3211679 0.3211679 0.3065693 0.3284672 0.2773723 0.3430657 0.2773723
14 0.3357664 0.3284672 0.3430657 0.3576642 0.2846715 0.3576642 0.2846715
15 0.3430657 0.3284672 0.3649635 0.3722628 0.2919708 0.3795620 0.3138686
   permut.29 permut.30 permut.31 permut.32 permut.33 permut.34 permut.35
1  0.2992701 0.2992701 0.2919708 0.2992701 0.2992701 0.2992701 0.2919708
2  0.2992701 0.2992701 0.2773723 0.2992701 0.2992701 0.2992701 0.2919708
3  0.2992701 0.2992701 0.2773723 0.2992701 0.2846715 0.2992701 0.2919708
4  0.2992701 0.2992701 0.2773723 0.2992701 0.2846715 0.2992701 0.2919708
5  0.2992701 0.2992701 0.2773723 0.2992701 0.2846715 0.2992701 0.2919708
6  0.2992701 0.2992701 0.2846715 0.2992701 0.2846715 0.2992701 0.2919708
7  0.2992701 0.2992701 0.2846715 0.2992701 0.2773723 0.2992701 0.2992701
8  0.3065693 0.2992701 0.2846715 0.2992701 0.2773723 0.2992701 0.2846715
9  0.3065693 0.3138686 0.2919708 0.2992701 0.2919708 0.2992701 0.2846715
10 0.3138686 0.3138686 0.3065693 0.2992701 0.2992701 0.2992701 0.2846715
11 0.3284672 0.3138686 0.3284672 0.3065693 0.2992701 0.3065693 0.2919708
12 0.3138686 0.3211679 0.3357664 0.3138686 0.3065693 0.3211679 0.2919708
13 0.3357664 0.3211679 0.3357664 0.3284672 0.3138686 0.3284672 0.3138686
14 0.3503650 0.3357664 0.3357664 0.3430657 0.3211679 0.3503650 0.3138686
15 0.3649635 0.3503650 0.3503650 0.3649635 0.3211679 0.3576642 0.3576642
   permut.36 permut.37 permut.38 permut.39 permut.40 permut.41 permut.42
1  0.2992701 0.2846715 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
2  0.2992701 0.2700730 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
3  0.2992701 0.2700730 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
4  0.2992701 0.2773723 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
5  0.2992701 0.2627737 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
6  0.2992701 0.2627737 0.2992701 0.2992701 0.2992701 0.2919708 0.2992701
7  0.2992701 0.2700730 0.2992701 0.2992701 0.2992701 0.2919708 0.2992701
8  0.2992701 0.2700730 0.3065693 0.3065693 0.3065693 0.2846715 0.2992701
9  0.2992701 0.2700730 0.3138686 0.3065693 0.3065693 0.2846715 0.3138686
10 0.2992701 0.2700730 0.3284672 0.3138686 0.3211679 0.2919708 0.3065693
11 0.3065693 0.2846715 0.3138686 0.3284672 0.3211679 0.3065693 0.3138686
12 0.3065693 0.2773723 0.3138686 0.3357664 0.3357664 0.2992701 0.3211679
13 0.3065693 0.2846715 0.3284672 0.3284672 0.3357664 0.3065693 0.3211679
14 0.3357664 0.2846715 0.3284672 0.3430657 0.3576642 0.3284672 0.3284672
15 0.3430657 0.3211679 0.3430657 0.3649635 0.3503650 0.3503650 0.3430657
   permut.43 permut.44 permut.45 permut.46 permut.47 permut.48 permut.49
1  0.2992701 0.2992701 0.2992701 0.2846715 0.2992701 0.2992701 0.2992701
2  0.2992701 0.2992701 0.2992701 0.2846715 0.2992701 0.2992701 0.2992701
3  0.2992701 0.2992701 0.2992701 0.2846715 0.2992701 0.2992701 0.2992701
4  0.2846715 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
5  0.2846715 0.2992701 0.2992701 0.2846715 0.3065693 0.2992701 0.2992701
6  0.2846715 0.3138686 0.2992701 0.2700730 0.2992701 0.2992701 0.2992701
7  0.2919708 0.3211679 0.2992701 0.2992701 0.3065693 0.2992701 0.2992701
8  0.2919708 0.3211679 0.2992701 0.2846715 0.2919708 0.2919708 0.2992701
9  0.2919708 0.3284672 0.2992701 0.2919708 0.2919708 0.2992701 0.3065693
10 0.2992701 0.3284672 0.2992701 0.2919708 0.2992701 0.2992701 0.3065693
11 0.2846715 0.3503650 0.3138686 0.2992701 0.3065693 0.3138686 0.3065693
12 0.2773723 0.3503650 0.3211679 0.3211679 0.3138686 0.2992701 0.3138686
13 0.2700730 0.3430657 0.3284672 0.3503650 0.3065693 0.2992701 0.3284672
14 0.2846715 0.3430657 0.3430657 0.3503650 0.2992701 0.3065693 0.3649635
15 0.3065693 0.3649635 0.3649635 0.3722628 0.3138686 0.3430657 0.3941606
   permut.50 permut.51 permut.52 permut.53 permut.54 permut.55 permut.56
1  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
2  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
3  0.2992701 0.2992701 0.2992701 0.2919708 0.2992701 0.2992701 0.2992701
4  0.2992701 0.2992701 0.2992701 0.2627737 0.2846715 0.2992701 0.2992701
5  0.2992701 0.2992701 0.2992701 0.2627737 0.2846715 0.2992701 0.2992701
6  0.2992701 0.2992701 0.2992701 0.2627737 0.2846715 0.2992701 0.2919708
7  0.2992701 0.2919708 0.3065693 0.2554745 0.2846715 0.3065693 0.2919708
8  0.2992701 0.2919708 0.2992701 0.2773723 0.2919708 0.2992701 0.2919708
9  0.2992701 0.2919708 0.2992701 0.2773723 0.2919708 0.2846715 0.3138686
10 0.2992701 0.2846715 0.2992701 0.2846715 0.2919708 0.2919708 0.3138686
11 0.2992701 0.2846715 0.3211679 0.2919708 0.2919708 0.2919708 0.3211679
12 0.2992701 0.3065693 0.3211679 0.2919708 0.3065693 0.3138686 0.3357664
13 0.3065693 0.3138686 0.3284672 0.2992701 0.2992701 0.3284672 0.3357664
14 0.3430657 0.3357664 0.3430657 0.3065693 0.2992701 0.3503650 0.3357664
15 0.3649635 0.3503650 0.3795620 0.2992701 0.3503650 0.3722628 0.3430657
   permut.57 permut.58 permut.59 permut.60 permut.61 permut.62 permut.63
1  0.2919708 0.2992701 0.2992701 0.2919708 0.2992701 0.2992701 0.2992701
2  0.2846715 0.2992701 0.2992701 0.2846715 0.2992701 0.2992701 0.2992701
3  0.2773723 0.2992701 0.2992701 0.2773723 0.2992701 0.2992701 0.2992701
4  0.2554745 0.2992701 0.2992701 0.2773723 0.2992701 0.2992701 0.2992701
5  0.2554745 0.2992701 0.2992701 0.2773723 0.2992701 0.3065693 0.2992701
6  0.2627737 0.2992701 0.2992701 0.2846715 0.2992701 0.3065693 0.2992701
7  0.2627737 0.2919708 0.3065693 0.2846715 0.2992701 0.3065693 0.2992701
8  0.2627737 0.2919708 0.3138686 0.2846715 0.2992701 0.3065693 0.2992701
9  0.2627737 0.2846715 0.3211679 0.2773723 0.3138686 0.3065693 0.3065693
10 0.2700730 0.2846715 0.3138686 0.2773723 0.3138686 0.3065693 0.3065693
11 0.2700730 0.2846715 0.3138686 0.3065693 0.3211679 0.3284672 0.3138686
12 0.2773723 0.2919708 0.3357664 0.3138686 0.3138686 0.3284672 0.3284672
13 0.2773723 0.2992701 0.3357664 0.3284672 0.3065693 0.3357664 0.3357664
14 0.2846715 0.3138686 0.3649635 0.3430657 0.3138686 0.3430657 0.3357664
15 0.3138686 0.3211679 0.3722628 0.3430657 0.3284672 0.3503650 0.3357664
   permut.64 permut.65 permut.66 permut.67 permut.68 permut.69 permut.70
1  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
2  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
3  0.2992701 0.2992701 0.2992701 0.2992701 0.2919708 0.2992701 0.2992701
4  0.2992701 0.2992701 0.2992701 0.2992701 0.2919708 0.2992701 0.2992701
5  0.2846715 0.2992701 0.2992701 0.2992701 0.2919708 0.2992701 0.2992701
6  0.2773723 0.2992701 0.3065693 0.2992701 0.2992701 0.2992701 0.2992701
7  0.2773723 0.2992701 0.3065693 0.2992701 0.2992701 0.2992701 0.2992701
8  0.2846715 0.2992701 0.2919708 0.2992701 0.3065693 0.2992701 0.2992701
9  0.2846715 0.2992701 0.2919708 0.2992701 0.3065693 0.2992701 0.2992701
10 0.2919708 0.2992701 0.2992701 0.3065693 0.3138686 0.3065693 0.2992701
11 0.2992701 0.2992701 0.2992701 0.3065693 0.3138686 0.3211679 0.3065693
12 0.3065693 0.3065693 0.3357664 0.2992701 0.3211679 0.3284672 0.3138686
13 0.3138686 0.3065693 0.3430657 0.3065693 0.3576642 0.3284672 0.3284672
14 0.3065693 0.3211679 0.3211679 0.3503650 0.3357664 0.3211679 0.3211679
15 0.3284672 0.3430657 0.3284672 0.3795620 0.3649635 0.3211679 0.3284672
   permut.71 permut.72 permut.73 permut.74 permut.75 permut.76 permut.77
1  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
2  0.2992701 0.2919708 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
3  0.2992701 0.2846715 0.2992701 0.2919708 0.2992701 0.2992701 0.2992701
4  0.2992701 0.2846715 0.2992701 0.2919708 0.2992701 0.2992701 0.2992701
5  0.2992701 0.2919708 0.2992701 0.2919708 0.2992701 0.2992701 0.2992701
6  0.2992701 0.2846715 0.2992701 0.2919708 0.2919708 0.2992701 0.2992701
7  0.2992701 0.2700730 0.3065693 0.2846715 0.2919708 0.2992701 0.2992701
8  0.2992701 0.2627737 0.3138686 0.2773723 0.2919708 0.2992701 0.3065693
9  0.3065693 0.2700730 0.3138686 0.2773723 0.2919708 0.3138686 0.3065693
10 0.3138686 0.2700730 0.3138686 0.2773723 0.2992701 0.3211679 0.3065693
11 0.3211679 0.2700730 0.3065693 0.2919708 0.2992701 0.3211679 0.3065693
12 0.3211679 0.2773723 0.3065693 0.2846715 0.3065693 0.2992701 0.3065693
13 0.3357664 0.2773723 0.3065693 0.2992701 0.3211679 0.3065693 0.3284672
14 0.3357664 0.2992701 0.3211679 0.3138686 0.3284672 0.3211679 0.3430657
15 0.3503650 0.3211679 0.3430657 0.3284672 0.3284672 0.3284672 0.3430657
   permut.78 permut.79 permut.80 permut.81 permut.82 permut.83 permut.84
1  0.2846715 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
2  0.2846715 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2773723
3  0.2773723 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2700730
4  0.2773723 0.2992701 0.2992701 0.2992701 0.2992701 0.2919708 0.2627737
5  0.2846715 0.2919708 0.2992701 0.2992701 0.2992701 0.2919708 0.2700730
6  0.2773723 0.2919708 0.2992701 0.2992701 0.2992701 0.2919708 0.2554745
7  0.2846715 0.2919708 0.2919708 0.2992701 0.2992701 0.2992701 0.2554745
8  0.2846715 0.2846715 0.2919708 0.2992701 0.2992701 0.3065693 0.2627737
9  0.2919708 0.2919708 0.2919708 0.3065693 0.2992701 0.3138686 0.2627737
10 0.2919708 0.2992701 0.2919708 0.3211679 0.3065693 0.3211679 0.2773723
11 0.2919708 0.2919708 0.3065693 0.3138686 0.3284672 0.3138686 0.2992701
12 0.3138686 0.3138686 0.3138686 0.2992701 0.3211679 0.3065693 0.3065693
13 0.3138686 0.3211679 0.3138686 0.2992701 0.3357664 0.3138686 0.3065693
14 0.3211679 0.3503650 0.3211679 0.3430657 0.3284672 0.3211679 0.3211679
15 0.3138686 0.3649635 0.3211679 0.3576642 0.3284672 0.3795620 0.3430657
   permut.85 permut.86 permut.87 permut.88 permut.89 permut.90 permut.91
1  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
2  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
3  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
4  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
5  0.2919708 0.2992701 0.2992701 0.3065693 0.2992701 0.2992701 0.2992701
6  0.2846715 0.2919708 0.2992701 0.3065693 0.2992701 0.2992701 0.2992701
7  0.2700730 0.2919708 0.2992701 0.3065693 0.2992701 0.2992701 0.2992701
8  0.2700730 0.2919708 0.2992701 0.3211679 0.3065693 0.2992701 0.2992701
9  0.2700730 0.2919708 0.2992701 0.3138686 0.2919708 0.2992701 0.2992701
10 0.2700730 0.2919708 0.3065693 0.3357664 0.2846715 0.2992701 0.2992701
11 0.2846715 0.2919708 0.3138686 0.3284672 0.2846715 0.2919708 0.2992701
12 0.2919708 0.3065693 0.3138686 0.3138686 0.2846715 0.3065693 0.3284672
13 0.3065693 0.3065693 0.3211679 0.3065693 0.3138686 0.3138686 0.3649635
14 0.3284672 0.3211679 0.3357664 0.2992701 0.3284672 0.3211679 0.3795620
15 0.3430657 0.3430657 0.3576642 0.2992701 0.3430657 0.3357664 0.3941606
   permut.92 permut.93 permut.94 permut.95 permut.96 permut.97 permut.98
1  0.2992701 0.2992701 0.2992701 0.2992701 0.2919708 0.2919708 0.2992701
2  0.2992701 0.2992701 0.2992701 0.2992701 0.2846715 0.2773723 0.2992701
3  0.2992701 0.2992701 0.2992701 0.2992701 0.2846715 0.2773723 0.2992701
4  0.2919708 0.2992701 0.2992701 0.2992701 0.2919708 0.2773723 0.2992701
5  0.2919708 0.2992701 0.3065693 0.2846715 0.2919708 0.2773723 0.2992701
6  0.2919708 0.3065693 0.3065693 0.2919708 0.2919708 0.2846715 0.2992701
7  0.2992701 0.3065693 0.2992701 0.2992701 0.2992701 0.2919708 0.2992701
8  0.2992701 0.3065693 0.2773723 0.3065693 0.3138686 0.2846715 0.2992701
9  0.3065693 0.3065693 0.2919708 0.2992701 0.3065693 0.2919708 0.2992701
10 0.3138686 0.3065693 0.2919708 0.3211679 0.3065693 0.3065693 0.3065693
11 0.3138686 0.3065693 0.2992701 0.3284672 0.3284672 0.3138686 0.3065693
12 0.3211679 0.3138686 0.2919708 0.3357664 0.3284672 0.3211679 0.3138686
13 0.3430657 0.3284672 0.2773723 0.3503650 0.3357664 0.3284672 0.3284672
14 0.3357664 0.3284672 0.2919708 0.3576642 0.3576642 0.3430657 0.3357664
15 0.3357664 0.3503650 0.3357664 0.3868613 0.3649635 0.3649635 0.3503650
   permut.99 permut.100  err.mean      err.sd    err.sterr
1  0.2992701  0.2846715 0.2977372 0.004187974 0.0004187974
2  0.2992701  0.2773723 0.2961314 0.007354726 0.0007354726
3  0.2992701  0.2627737 0.2945985 0.009925099 0.0009925099
4  0.2992701  0.2481752 0.2934307 0.011645606 0.0011645606
5  0.2992701  0.2189781 0.2929927 0.013286948 0.0013286948
6  0.2992701  0.2189781 0.2935036 0.013578418 0.0013578418
7  0.2992701  0.2262774 0.2940146 0.013450389 0.0013450389
8  0.2992701  0.2408759 0.2950365 0.013887421 0.0013887421
9  0.2992701  0.2481752 0.2975182 0.014229653 0.0014229653
10 0.3065693  0.2700730 0.3003650 0.015678377 0.0015678377
11 0.3065693  0.2627737 0.3062774 0.017202042 0.0017202042
12 0.3065693  0.2700730 0.3114599 0.018444130 0.0018444130
13 0.3138686  0.2846715 0.3189051 0.020215955 0.0020215955
14 0.3211679  0.2773723 0.3296350 0.021656117 0.0021656117
15 0.3357664  0.2773723 0.3445255 0.023566858 0.0023566858

$permut.stepwise.lda$best.p
[1] 6

$permut.stepwise.lda$best.error
[1] 0.2189781

$permut.stepwise.lda$best.pda
$permut.stepwise.lda$best.pda$class
  [1] PHO CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL PHO CTL
 [19] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL
 [37] CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL PHO CTL CTL CTL CTL CTL
 [55] CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
 [73] CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL PHO
 [91] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL PHO CTL PHO CTL CTL
[109] CTL CTL CTL CTL CTL PHO CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[127] CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL
Levels: CTL PHO

$permut.stepwise.lda$best.pda$posterior
                 CTL        PHO
YAL002W   0.37951976 0.62048024
YAL038W   0.62786766 0.37213234
YAR064W   0.79368831 0.20631169
YAR070C   0.30855860 0.69144140
YAR071W   0.89799859 0.10200141
YBL005W   0.75258941 0.24741059
YBL030C   0.57656527 0.42343473
YBR006W   0.52836474 0.47163526
YBR018C   0.88305644 0.11694356
YBR020W   0.80779442 0.19220558
YBR093C   0.65622932 0.34377068
YBR115C   0.74401782 0.25598218
YBR184W   0.92770279 0.07229721
YBR213W   0.88614669 0.11385331
YBR296C   0.32321793 0.67678207
YCL018W   0.66262787 0.33737213
YCR037C   0.05176762 0.94823238
YCR098C   0.69939361 0.30060639
YDL131W   0.72850359 0.27149641
YDL182W   0.92235364 0.07764636
YDL205C   0.85107619 0.14892381
YDL210W   0.79468671 0.20531329
YDR011W   0.86598059 0.13401941
YDR041W   0.61980862 0.38019138
YDR044W   0.60513489 0.39486511
YDR054C   0.84696934 0.15303066
YDR055W   0.88077549 0.11922451
YDR169C   0.64745294 0.35254706
YDR234W   0.81134163 0.18865837
YDR281C   0.72333496 0.27666504
YDR285W   0.76357054 0.23642946
YDR303C   0.66379005 0.33620995
YDR310C   0.70091259 0.29908741
YDR311W   0.83616605 0.16383395
YDR406W   0.48914849 0.51085151
YDR481C   0.78787918 0.21212082
YDR502C   0.75844264 0.24155736
YEL017C-A 0.84381683 0.15618317
YEL017W   0.72057395 0.27942605
YEL021W   0.68591718 0.31408282
YEL039C   0.79811739 0.20188261
YEL045C   0.61854148 0.38145852
YER017C   0.85476800 0.14523200
YER019W   0.79428106 0.20571894
YER026C   0.47389762 0.52610238
YER073W   0.76614944 0.23385056
YER086W   0.52813473 0.47186527
YER091C   0.80034778 0.19965222
YER179W   0.41470450 0.58529550
YFL004W   0.83312286 0.16687714
YFR030W   0.84322079 0.15677921
YGL009C   0.54257932 0.45742068
YGL073W   0.74186179 0.25813821
YGL213C   0.74524731 0.25475269
YGR019W   0.54768549 0.45231451
YGR044C   0.58013761 0.41986239
YGR088W   0.77020236 0.22979764
YGR121C   0.70378418 0.29621582
YGR157W   0.94385932 0.05614068
YGR233C   0.88777057 0.11222943
YGR281W   0.44139998 0.55860002
YHL022C   0.69223765 0.30776235
YHL036W   0.98228777 0.01771223
YHR007C   0.66701094 0.33298906
YHR008C   0.81439032 0.18560968
YHR014W   0.52856068 0.47143932
YHR037W   0.72660211 0.27339789
YHR136C   0.69725344 0.30274656
YHR137W   0.65748015 0.34251985
YHR153C   0.74135538 0.25864462
YHR168W   0.74109475 0.25890525
YHR215W   0.92386181 0.07613819
YIL015W   0.71236628 0.28763372
YIL046W   0.55006853 0.44993147
YIL072W   0.25708174 0.74291826
YIR017C   0.86438214 0.13561786
YIR034C   0.75980677 0.24019323
YJL012C   0.81443752 0.18556248
YJL106W   0.77359203 0.22640797
YJL117W   0.95905132 0.04094868
YJL153C   0.51435008 0.48564992
YJL209W   0.84639440 0.15360560
YJL211C   0.86425954 0.13574046
YJL219W   0.69072333 0.30927667
YJR010W   0.17616553 0.82383447
YJR048W   0.55247397 0.44752603
YJR073C   0.53629986 0.46370014
YJR094C   0.63230281 0.36769719
YJR137C   0.85994328 0.14005672
YJR152W   0.39759171 0.60240829
YKL001C   0.99086947 0.00913053
YKL182W   0.76579475 0.23420525
YKL216W   0.75376558 0.24623442
YKR039W   0.58602004 0.41397996
YKR048C   0.57103116 0.42896884
YKR050W   0.57103116 0.42896884
YKR069W   0.93176319 0.06823681
YLR081W   0.61370709 0.38629291
YLR142W   0.56335807 0.43664193
YLR180W   0.77548226 0.22451774
YLR263W   0.15927092 0.84072908
YLR303W   0.79308488 0.20691512
YLR329W   0.87438292 0.12561708
YLR420W   0.49112248 0.50887752
YLR438W   0.79535769 0.20464231
YML051W   0.43094708 0.56905292
YML054C   0.76389310 0.23610690
YML075C   0.69979547 0.30020453
YML121W   0.78497374 0.21502626
YML123C   0.81705625 0.18294375
YMR108W   0.84512550 0.15487450
YMR133W   0.70344350 0.29655650
YNL052W   0.77735549 0.22264451
YNL061W   0.47655702 0.52344298
YNL063W   0.60566127 0.39433873
YNL064C   0.59879335 0.40120665
YNL104C   0.82205341 0.17794659
YNL142W   0.47997582 0.52002418
YNL210W   0.89849632 0.10150368
YNL241C   0.87144423 0.12855577
YNL277W   0.70414917 0.29585083
YNR001C   0.77767438 0.22232562
YNR050C   0.88097210 0.11902790
YOL006C   0.89997159 0.10002841
YOR065W   0.94913985 0.05086015
YOR120W   0.73203434 0.26796566
YOR153W   0.73221723 0.26778277
YOR328W   0.64259792 0.35740208
YOR351C   0.92925986 0.07074014
YOR375C   0.67507570 0.32492430
YPL068C   0.77043736 0.22956264
YPL111W   0.87834985 0.12165015
YPL231W   0.46538105 0.53461895
YPR065W   0.90950440 0.09049560
YPR138C   0.53611995 0.46388005
YPR145W   0.94329040 0.05670960
YPR167C   0.89442171 0.10557829

$permut.stepwise.lda$best.pda$call
lda(x = data.training, grouping = labels.training, CV = loo, 
    na.action = na.omit)

$permut.stepwise.lda$best.pda$training.label
  [1] PHO CTL CTL PHO CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL PHO PHO PHO PHO
 [19] CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL
 [37] CTL PHO PHO CTL CTL CTL CTL PHO PHO CTL CTL CTL PHO PHO CTL CTL CTL PHO
 [55] PHO CTL CTL CTL CTL PHO PHO CTL PHO CTL CTL PHO CTL PHO CTL PHO PHO PHO
 [73] PHO CTL PHO CTL CTL CTL CTL CTL CTL CTL PHO CTL PHO CTL CTL CTL PHO CTL
 [91] CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL
[109] CTL CTL CTL CTL PHO PHO PHO CTL CTL PHO PHO CTL CTL PHO CTL PHO CTL CTL
[127] CTL CTL CTL PHO CTL CTL PHO CTL CTL CTL CTL
Levels: CTL PHO

$permut.stepwise.lda$best.pda$pda.method
[1] "lda"

$permut.stepwise.lda$best.pda$loo
[1] TRUE

$permut.stepwise.lda$best.pda$validation
[1] "LOO"

$permut.stepwise.lda$best.pda$confusion
      true
object CTL PHO
   CTL  93  27
   PHO   3  14
attr(,"error")
[1] 0.2189781



$permut.pc.stepwise.lda
$permut.pc.stepwise.lda$confusion.table
        error CTL.CTL CTL.PHO PHO.CTL PHO.PHO
1   0.2700730      91       5      32       9
2   0.2919708      95       1      39       2
3   0.2846715      96       0      39       2
4   0.2992701      96       0      41       0
5   0.2846715      94       2      37       4
6   0.2554745      92       4      31      10
7   0.2992701      96       0      41       0
8   0.2992701      96       0      41       0
9   0.2627737      88       8      28      13
10  0.2481752      93       3      31      10
11  0.2992701      95       1      40       1
12  0.2846715      96       0      39       2
13  0.2846715      96       0      39       2
14  0.2992701      96       0      41       0
15  0.2846715      91       5      34       7
16  0.2992701      96       0      41       0
17  0.2992701      96       0      41       0
18  0.2773723      94       2      36       5
19  0.2919708      96       0      40       1
20  0.2992701      96       0      41       0
21  0.2554745      95       1      34       7
22  0.2773723      95       1      37       4
23  0.2919708      96       0      40       1
24  0.2773723      96       0      38       3
25  0.2992701      86      10      31      10
26  0.2992701      96       0      41       0
27  0.2992701      96       0      41       0
28  0.2992701      96       0      41       0
29  0.2919708      96       0      40       1
30  0.2773723      93       3      35       6
31  0.2846715      93       3      36       5
32  0.2919708      86      10      30      11
33  0.2992701      91       5      36       5
34  0.2846715      95       1      38       3
35  0.2627737      88       8      28      13
36  0.2992701      93       3      38       3
37  0.2262774      92       4      27      14
38  0.2700730      89       7      30      11
39  0.2846715      90       6      33       8
40  0.2992701      96       0      41       0
41  0.2919708      95       1      39       2
42  0.2992701      96       0      41       0
43  0.2992701      96       0      41       0
44  0.2481752      93       3      31      10
45  0.2992701      96       0      41       0
46  0.2992701      96       0      41       0
47  0.2992701      96       0      41       0
48  0.2554745      94       2      33       8
49  0.2992701      96       0      41       0
50  0.2992701      96       0      41       0
51  0.2992701      96       0      41       0
52  0.2846715      95       1      38       3
53  0.2992701      93       3      38       3
54  0.2627737      90       6      30      11
55  0.2919708      94       2      38       3
56  0.2919708      95       1      39       2
57  0.2992701      96       0      41       0
58  0.2700730      96       0      37       4
59  0.2846715      95       1      38       3
60  0.2846715      95       1      38       3
61  0.2992701      96       0      41       0
62  0.2773723      96       0      38       3
63  0.2992701      96       0      41       0
64  0.2919708      95       1      39       2
65  0.2992701      96       0      41       0
66  0.2700730      93       3      34       7
67  0.2773723      91       5      33       8
68  0.2992701      96       0      41       0
69  0.2992701      96       0      41       0
70  0.2554745      94       2      33       8
71  0.2846715      90       6      33       8
72  0.2846715      93       3      36       5
73  0.2481752      96       0      34       7
74  0.2846715      94       2      37       4
75  0.2992701      96       0      41       0
76  0.2992701      96       0      41       0
77  0.2992701      96       0      41       0
78  0.2992701      96       0      41       0
79  0.2846715      95       1      38       3
80  0.2919708      89       7      33       8
81  0.2554745      96       0      35       6
82  0.2992701      96       0      41       0
83  0.2554745      92       4      31      10
84  0.2773723      93       3      35       6
85  0.2992701      96       0      41       0
86  0.2992701      96       0      41       0
87  0.2773723      88       8      30      11
88  0.2773723      94       2      36       5
89  0.2992701      96       0      41       0
90  0.2846715      95       1      38       3
91  0.2700730      88       8      29      12
92  0.2846715      96       0      39       2
93  0.2992701      96       0      41       0
94  0.2846715      93       3      36       5
95  0.2992701      96       0      41       0
96  0.2919708      96       0      40       1
97  0.2919708      93       3      37       4
98  0.2919708      88       8      32       9
99  0.2700730      94       2      35       6
100 0.2992701      96       0      41       0

$permut.pc.stepwise.lda$errors
    permut.1  permut.2  permut.3  permut.4  permut.5  permut.6  permut.7
1  0.2773723 0.2992701 0.2992701 0.2992701 0.2992701 0.2919708 0.2992701
2  0.2700730 0.2992701 0.2846715 0.2992701 0.2919708 0.2554745 0.2992701
3  0.2700730 0.2992701 0.2846715 0.2992701 0.2846715 0.2554745 0.2992701
4  0.2700730 0.2992701 0.2846715 0.2992701 0.2846715 0.2554745 0.2992701
5  0.2700730 0.2919708 0.2846715 0.2992701 0.2846715 0.2554745 0.2992701
6  0.2700730 0.2919708 0.2846715 0.2992701 0.2846715 0.2627737 0.2992701
7  0.2700730 0.2919708 0.2846715 0.2992701 0.2919708 0.2627737 0.2992701
8  0.2700730 0.2919708 0.2846715 0.2992701 0.3065693 0.2627737 0.2992701
9  0.2773723 0.2919708 0.2919708 0.2992701 0.2992701 0.2627737 0.2992701
10 0.2846715 0.2992701 0.2919708 0.3065693 0.2992701 0.2773723 0.2992701
11 0.2846715 0.3065693 0.3065693 0.3065693 0.3065693 0.2773723 0.3065693
12 0.2992701 0.3211679 0.2992701 0.3284672 0.3065693 0.2773723 0.3138686
13 0.3065693 0.3357664 0.3138686 0.3430657 0.3065693 0.2773723 0.3503650
14 0.3211679 0.3430657 0.3649635 0.3503650 0.3065693 0.2773723 0.3503650
15 0.3430657 0.3649635 0.3649635 0.3649635 0.3357664 0.3065693 0.3941606
    permut.8  permut.9 permut.10 permut.11 permut.12 permut.13 permut.14
1  0.2992701 0.2919708 0.2700730 0.2992701 0.2919708 0.2846715 0.2992701
2  0.2992701 0.2773723 0.2627737 0.2992701 0.2846715 0.2846715 0.2992701
3  0.2992701 0.2627737 0.2481752 0.2992701 0.2846715 0.2846715 0.2992701
4  0.2992701 0.2627737 0.2481752 0.2992701 0.2846715 0.2846715 0.2992701
5  0.2992701 0.2627737 0.2554745 0.2992701 0.2846715 0.2919708 0.2992701
6  0.2992701 0.2627737 0.2554745 0.2992701 0.2919708 0.2919708 0.2992701
7  0.2992701 0.2627737 0.2554745 0.2992701 0.2846715 0.2846715 0.2992701
8  0.3065693 0.2627737 0.2481752 0.2992701 0.2846715 0.2846715 0.2992701
9  0.3138686 0.2627737 0.2481752 0.2992701 0.2992701 0.2846715 0.3065693
10 0.3065693 0.2700730 0.2627737 0.3065693 0.3138686 0.2846715 0.3211679
11 0.3211679 0.2700730 0.2700730 0.3065693 0.3357664 0.2919708 0.3284672
12 0.3211679 0.2773723 0.2846715 0.3284672 0.3430657 0.2919708 0.3357664
13 0.3503650 0.2773723 0.2992701 0.3576642 0.3430657 0.3065693 0.3430657
14 0.3503650 0.2846715 0.3284672 0.3576642 0.3503650 0.3065693 0.3576642
15 0.3503650 0.2992701 0.3284672 0.4014599 0.3722628 0.3138686 0.3868613
   permut.15 permut.16 permut.17 permut.18 permut.19 permut.20 permut.21
1  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2700730
2  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2627737
3  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2554745
4  0.2846715 0.2992701 0.2992701 0.2992701 0.2919708 0.2992701 0.2554745
5  0.2846715 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2554745
6  0.2846715 0.3065693 0.2992701 0.2773723 0.2992701 0.2992701 0.2627737
7  0.2846715 0.3065693 0.2992701 0.2773723 0.2992701 0.2992701 0.2627737
8  0.2846715 0.3065693 0.2992701 0.2773723 0.2992701 0.2992701 0.2700730
9  0.2919708 0.3065693 0.2992701 0.2773723 0.2992701 0.3065693 0.2700730
10 0.2992701 0.3138686 0.2992701 0.2846715 0.3065693 0.3065693 0.2919708
11 0.3065693 0.3211679 0.2992701 0.2992701 0.3138686 0.3138686 0.2700730
12 0.3211679 0.3284672 0.3065693 0.3065693 0.3138686 0.3211679 0.2773723
13 0.3065693 0.3430657 0.3138686 0.3138686 0.3138686 0.3357664 0.2992701
14 0.3357664 0.3503650 0.3357664 0.3211679 0.3138686 0.3576642 0.2919708
15 0.3503650 0.3868613 0.3722628 0.3211679 0.3430657 0.3430657 0.3211679
   permut.22 permut.23 permut.24 permut.25 permut.26 permut.27 permut.28
1  0.2919708 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
2  0.2846715 0.2992701 0.2846715 0.2992701 0.2992701 0.2992701 0.2992701
3  0.2773723 0.2992701 0.2846715 0.2992701 0.2992701 0.2992701 0.2992701
4  0.2773723 0.2992701 0.2846715 0.2992701 0.2992701 0.2992701 0.2992701
5  0.2773723 0.2992701 0.2846715 0.2992701 0.2992701 0.2992701 0.2992701
6  0.2773723 0.2992701 0.2773723 0.2992701 0.2992701 0.2992701 0.2992701
7  0.2846715 0.2992701 0.2773723 0.2992701 0.2992701 0.2992701 0.3065693
8  0.2919708 0.2919708 0.2773723 0.2992701 0.2992701 0.2992701 0.3138686
9  0.2992701 0.2992701 0.2919708 0.2992701 0.2992701 0.2992701 0.3138686
10 0.3138686 0.2992701 0.2992701 0.2992701 0.3065693 0.2992701 0.3211679
11 0.3284672 0.3065693 0.3065693 0.3138686 0.3138686 0.3138686 0.3211679
12 0.3284672 0.3138686 0.3138686 0.3065693 0.3211679 0.3211679 0.3284672
13 0.3430657 0.3357664 0.3284672 0.2992701 0.3357664 0.3284672 0.3357664
14 0.3503650 0.3284672 0.3211679 0.2992701 0.3284672 0.3357664 0.3576642
15 0.3430657 0.3576642 0.3503650 0.3284672 0.3649635 0.3649635 0.3649635
   permut.29 permut.30 permut.31 permut.32 permut.33 permut.34 permut.35
1  0.2992701 0.2992701 0.2919708 0.2992701 0.2992701 0.2992701 0.2846715
2  0.2992701 0.2992701 0.2919708 0.2992701 0.2992701 0.2992701 0.2773723
3  0.2992701 0.2992701 0.2846715 0.2919708 0.2992701 0.2846715 0.2700730
4  0.2992701 0.2992701 0.2846715 0.2919708 0.2992701 0.2846715 0.2700730
5  0.2992701 0.2992701 0.2919708 0.2992701 0.2992701 0.2846715 0.2627737
6  0.2992701 0.2919708 0.2992701 0.3065693 0.2992701 0.2919708 0.2627737
7  0.2992701 0.2773723 0.3065693 0.3138686 0.2992701 0.2919708 0.2700730
8  0.2992701 0.2919708 0.3065693 0.3138686 0.3065693 0.2919708 0.2773723
9  0.2919708 0.2992701 0.3065693 0.2992701 0.2992701 0.2919708 0.2846715
10 0.2919708 0.2992701 0.3138686 0.2919708 0.2992701 0.2919708 0.2919708
11 0.2992701 0.2992701 0.3211679 0.2919708 0.3065693 0.3065693 0.2992701
12 0.2992701 0.2992701 0.3211679 0.2919708 0.3138686 0.3065693 0.2992701
13 0.3138686 0.3211679 0.3284672 0.3065693 0.3357664 0.3065693 0.3065693
14 0.3211679 0.3284672 0.3430657 0.2992701 0.3430657 0.3357664 0.3065693
15 0.3430657 0.3649635 0.3503650 0.3211679 0.3503650 0.3649635 0.3211679
   permut.36 permut.37 permut.38 permut.39 permut.40 permut.41 permut.42
1  0.2992701 0.2700730 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
2  0.2992701 0.2554745 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
3  0.2992701 0.2481752 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
4  0.2992701 0.2335766 0.2992701 0.2919708 0.2992701 0.2919708 0.2992701
5  0.3065693 0.2262774 0.2992701 0.2992701 0.2992701 0.2919708 0.2992701
6  0.3065693 0.2262774 0.2992701 0.2846715 0.2992701 0.2919708 0.2992701
7  0.3065693 0.2335766 0.2992701 0.2919708 0.2992701 0.2992701 0.2992701
8  0.3065693 0.2262774 0.2919708 0.2992701 0.2992701 0.2919708 0.2992701
9  0.3138686 0.2408759 0.2773723 0.2919708 0.2992701 0.2919708 0.3065693
10 0.3065693 0.2335766 0.2919708 0.3065693 0.3065693 0.2992701 0.3138686
11 0.3065693 0.2335766 0.2773723 0.3138686 0.3138686 0.2992701 0.3138686
12 0.2992701 0.2335766 0.2773723 0.3138686 0.3284672 0.3138686 0.3211679
13 0.3211679 0.2408759 0.2773723 0.3284672 0.3211679 0.3211679 0.3357664
14 0.3503650 0.2408759 0.2700730 0.3211679 0.3430657 0.3211679 0.3503650
15 0.3211679 0.2627737 0.2919708 0.3722628 0.3722628 0.3576642 0.3357664
   permut.43 permut.44 permut.45 permut.46 permut.47 permut.48 permut.49
1  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
2  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2919708 0.2992701
3  0.2992701 0.2773723 0.2992701 0.2992701 0.2992701 0.2919708 0.2992701
4  0.2992701 0.2554745 0.2992701 0.2992701 0.2992701 0.2773723 0.2992701
5  0.2992701 0.2481752 0.2992701 0.2992701 0.2992701 0.2700730 0.2992701
6  0.2992701 0.2554745 0.2992701 0.2992701 0.2992701 0.2627737 0.2992701
7  0.2992701 0.2627737 0.2992701 0.2992701 0.2992701 0.2773723 0.2992701
8  0.3065693 0.2627737 0.2992701 0.3065693 0.2992701 0.2627737 0.2992701
9  0.3065693 0.2627737 0.2992701 0.3138686 0.2992701 0.2627737 0.2992701
10 0.3138686 0.2700730 0.3065693 0.3138686 0.3065693 0.2554745 0.2992701
11 0.3065693 0.2773723 0.3138686 0.3284672 0.3138686 0.2773723 0.2992701
12 0.3211679 0.2773723 0.3065693 0.3211679 0.3138686 0.2992701 0.3065693
13 0.3430657 0.2846715 0.3357664 0.3284672 0.3357664 0.3138686 0.3430657
14 0.3357664 0.2919708 0.3357664 0.3284672 0.3503650 0.3357664 0.3430657
15 0.3576642 0.2992701 0.3357664 0.3138686 0.3576642 0.3357664 0.3868613
   permut.50 permut.51 permut.52 permut.53 permut.54 permut.55 permut.56
1  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
2  0.2992701 0.2992701 0.2992701 0.2992701 0.2919708 0.2992701 0.2992701
3  0.2992701 0.2992701 0.2992701 0.2992701 0.2919708 0.2992701 0.2992701
4  0.2992701 0.2992701 0.2846715 0.2992701 0.2846715 0.2992701 0.2992701
5  0.2992701 0.2992701 0.2846715 0.2992701 0.2700730 0.2992701 0.2992701
6  0.2992701 0.3065693 0.2846715 0.2992701 0.2627737 0.2992701 0.2919708
7  0.2992701 0.3065693 0.2846715 0.2992701 0.2700730 0.2992701 0.2919708
8  0.2992701 0.3138686 0.2919708 0.2992701 0.2773723 0.2919708 0.2919708
9  0.3065693 0.3138686 0.2919708 0.2992701 0.2846715 0.2919708 0.2919708
10 0.3065693 0.3284672 0.3065693 0.2992701 0.2846715 0.2992701 0.2992701
11 0.3065693 0.3357664 0.3138686 0.3211679 0.2846715 0.2992701 0.2992701
12 0.3211679 0.3357664 0.3211679 0.3284672 0.2919708 0.2992701 0.3138686
13 0.3211679 0.3357664 0.3284672 0.3430657 0.2919708 0.3211679 0.3138686
14 0.3430657 0.3357664 0.3503650 0.3430657 0.3138686 0.3284672 0.3211679
15 0.3722628 0.3576642 0.3795620 0.3430657 0.3065693 0.3503650 0.3357664
   permut.57 permut.58 permut.59 permut.60 permut.61 permut.62 permut.63
1  0.2992701 0.2992701 0.2919708 0.2992701 0.2992701 0.2992701 0.2992701
2  0.2992701 0.2773723 0.2846715 0.2992701 0.2992701 0.2992701 0.2992701
3  0.2992701 0.2700730 0.2846715 0.2919708 0.2992701 0.2919708 0.2992701
4  0.2992701 0.2700730 0.2846715 0.2919708 0.2992701 0.2919708 0.2992701
5  0.2992701 0.2700730 0.2846715 0.2846715 0.2992701 0.2773723 0.2992701
6  0.2992701 0.2700730 0.2846715 0.2846715 0.2992701 0.2773723 0.2992701
7  0.2992701 0.2700730 0.2919708 0.2919708 0.2992701 0.2773723 0.2992701
8  0.3065693 0.2773723 0.2919708 0.2919708 0.2992701 0.2846715 0.2992701
9  0.3065693 0.2919708 0.2919708 0.2992701 0.2992701 0.2846715 0.2992701
10 0.3065693 0.2919708 0.3065693 0.3138686 0.2992701 0.2919708 0.2992701
11 0.3065693 0.2846715 0.3211679 0.3138686 0.3065693 0.2992701 0.3065693
12 0.3138686 0.2919708 0.3138686 0.3211679 0.3284672 0.3065693 0.3065693
13 0.3211679 0.2919708 0.3284672 0.3284672 0.3357664 0.3284672 0.3065693
14 0.3430657 0.3138686 0.3284672 0.3430657 0.3576642 0.3357664 0.3284672
15 0.3576642 0.3211679 0.3357664 0.3576642 0.3722628 0.3503650 0.3138686
   permut.64 permut.65 permut.66 permut.67 permut.68 permut.69 permut.70
1  0.2919708 0.2992701 0.2919708 0.2992701 0.2992701 0.2992701 0.2846715
2  0.2919708 0.2992701 0.2773723 0.2992701 0.2992701 0.2992701 0.2627737
3  0.2919708 0.2992701 0.2700730 0.2846715 0.2992701 0.2992701 0.2554745
4  0.2919708 0.2992701 0.2700730 0.2773723 0.2992701 0.2992701 0.2554745
5  0.2919708 0.2992701 0.2700730 0.2773723 0.2992701 0.2992701 0.2554745
6  0.2919708 0.2992701 0.2700730 0.2773723 0.2992701 0.2992701 0.2554745
7  0.2919708 0.2992701 0.2773723 0.2773723 0.2992701 0.2992701 0.2554745
8  0.2992701 0.2992701 0.2773723 0.2773723 0.2992701 0.3065693 0.2554745
9  0.3065693 0.2992701 0.2846715 0.2773723 0.3065693 0.3138686 0.2627737
10 0.3065693 0.2992701 0.2919708 0.2919708 0.3138686 0.3211679 0.2773723
11 0.3065693 0.2992701 0.2992701 0.2992701 0.3284672 0.3211679 0.2773723
12 0.3138686 0.3065693 0.3211679 0.3138686 0.3211679 0.3284672 0.2846715
13 0.3284672 0.3138686 0.3284672 0.3138686 0.3357664 0.3138686 0.3138686
14 0.3430657 0.3211679 0.3357664 0.3430657 0.3357664 0.3138686 0.3138686
15 0.3503650 0.3430657 0.3357664 0.3503650 0.3576642 0.3357664 0.3138686
   permut.71 permut.72 permut.73 permut.74 permut.75 permut.76 permut.77
1  0.2992701 0.2846715 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
2  0.2992701 0.2919708 0.2919708 0.2992701 0.2992701 0.2992701 0.2992701
3  0.2992701 0.2919708 0.2773723 0.2992701 0.2992701 0.2992701 0.2992701
4  0.2992701 0.2919708 0.2773723 0.2919708 0.2992701 0.2992701 0.2992701
5  0.2992701 0.2992701 0.2700730 0.2846715 0.2992701 0.2992701 0.2992701
6  0.3065693 0.3065693 0.2700730 0.2992701 0.2992701 0.2992701 0.3065693
7  0.2992701 0.3065693 0.2481752 0.2992701 0.2992701 0.2992701 0.3138686
8  0.2846715 0.3138686 0.2554745 0.3065693 0.2992701 0.3065693 0.3211679
9  0.2919708 0.3138686 0.2554745 0.3065693 0.2992701 0.3065693 0.3211679
10 0.2846715 0.3138686 0.2700730 0.3138686 0.3138686 0.3065693 0.3211679
11 0.2846715 0.3211679 0.2846715 0.3211679 0.3211679 0.3138686 0.3211679
12 0.2919708 0.3284672 0.2846715 0.3284672 0.3284672 0.3211679 0.3284672
13 0.2992701 0.3430657 0.3065693 0.3576642 0.3211679 0.3503650 0.3284672
14 0.2992701 0.3649635 0.2992701 0.3722628 0.3284672 0.3430657 0.3503650
15 0.3211679 0.3649635 0.3065693 0.3868613 0.3357664 0.3649635 0.3430657
   permut.78 permut.79 permut.80 permut.81 permut.82 permut.83 permut.84
1  0.2992701 0.2992701 0.2992701 0.2919708 0.2992701 0.2846715 0.2992701
2  0.2992701 0.2919708 0.2992701 0.2846715 0.2992701 0.2773723 0.2992701
3  0.2992701 0.2846715 0.2992701 0.2627737 0.2992701 0.2627737 0.2992701
4  0.2992701 0.2846715 0.2992701 0.2554745 0.2992701 0.2627737 0.2919708
5  0.2992701 0.2846715 0.2992701 0.2554745 0.2992701 0.2627737 0.2846715
6  0.2992701 0.2846715 0.2992701 0.2627737 0.2992701 0.2554745 0.2773723
7  0.3065693 0.2919708 0.2992701 0.2773723 0.2992701 0.2554745 0.2773723
8  0.3138686 0.2919708 0.3065693 0.2846715 0.2992701 0.2554745 0.2773723
9  0.3138686 0.2919708 0.2919708 0.2919708 0.2992701 0.2554745 0.2773723
10 0.3284672 0.3065693 0.2919708 0.3065693 0.3138686 0.2700730 0.2919708
11 0.3211679 0.3138686 0.2919708 0.3138686 0.3211679 0.2846715 0.2919708
12 0.3211679 0.3211679 0.3065693 0.3284672 0.3357664 0.2846715 0.3065693
13 0.3357664 0.3430657 0.3065693 0.3211679 0.3357664 0.2992701 0.3284672
14 0.3576642 0.3503650 0.3138686 0.3284672 0.3503650 0.3065693 0.3357664
15 0.3576642 0.3795620 0.3649635 0.3503650 0.3430657 0.3357664 0.3503650
   permut.85 permut.86 permut.87 permut.88 permut.89 permut.90 permut.91
1  0.2992701 0.2992701 0.2846715 0.2992701 0.2992701 0.2992701 0.2919708
2  0.2992701 0.2992701 0.2846715 0.2992701 0.2992701 0.2919708 0.2846715
3  0.2992701 0.2992701 0.2846715 0.2992701 0.2992701 0.2919708 0.2846715
4  0.2992701 0.2992701 0.2846715 0.2919708 0.2992701 0.2919708 0.2846715
5  0.2992701 0.2992701 0.2846715 0.2919708 0.2992701 0.2992701 0.2919708
6  0.2992701 0.2992701 0.2919708 0.2992701 0.2992701 0.2919708 0.2773723
7  0.2992701 0.2992701 0.2919708 0.2919708 0.2992701 0.2846715 0.2700730
8  0.2992701 0.3065693 0.2773723 0.2773723 0.2992701 0.2919708 0.2700730
9  0.3065693 0.3065693 0.2846715 0.2773723 0.3065693 0.2919708 0.2700730
10 0.3138686 0.3065693 0.2992701 0.2773723 0.3065693 0.2919708 0.2700730
11 0.3284672 0.3138686 0.2992701 0.2919708 0.3065693 0.3065693 0.2846715
12 0.3357664 0.3211679 0.3138686 0.3065693 0.3138686 0.2992701 0.2919708
13 0.3430657 0.3284672 0.3138686 0.3138686 0.3138686 0.2992701 0.2919708
14 0.3649635 0.3430657 0.3138686 0.3138686 0.3430657 0.2992701 0.2992701
15 0.3722628 0.3503650 0.3138686 0.3211679 0.3430657 0.3284672 0.3065693
   permut.92 permut.93 permut.94 permut.95 permut.96 permut.97 permut.98
1  0.2992701 0.2992701 0.2992701 0.2992701 0.2919708 0.2992701 0.2992701
2  0.2992701 0.2992701 0.2992701 0.2992701 0.2919708 0.2992701 0.2992701
3  0.2992701 0.2992701 0.2919708 0.2992701 0.2919708 0.2992701 0.2992701
4  0.2992701 0.2992701 0.2846715 0.2992701 0.2919708 0.2919708 0.2992701
5  0.2992701 0.2992701 0.2846715 0.2992701 0.3065693 0.2919708 0.2992701
6  0.2992701 0.2992701 0.2846715 0.2992701 0.3065693 0.2919708 0.2992701
7  0.2846715 0.2992701 0.2846715 0.2992701 0.3138686 0.2992701 0.2992701
8  0.2846715 0.2992701 0.2992701 0.2992701 0.3138686 0.2992701 0.2992701
9  0.2846715 0.3065693 0.3065693 0.2992701 0.3211679 0.2992701 0.2992701
10 0.2992701 0.3065693 0.2919708 0.2992701 0.3284672 0.2992701 0.2992701
11 0.3065693 0.3065693 0.3065693 0.3065693 0.3357664 0.2919708 0.2992701
12 0.3138686 0.3138686 0.3065693 0.3138686 0.3430657 0.2992701 0.2919708
13 0.3138686 0.3284672 0.3138686 0.3138686 0.3503650 0.3211679 0.2992701
14 0.2992701 0.3430657 0.3430657 0.3284672 0.3649635 0.3357664 0.3138686
15 0.3284672 0.3649635 0.3576642 0.3357664 0.3795620 0.3430657 0.2992701
   permut.99 permut.100  err.mean     err.sd   err.sterr
1  0.2919708  0.2992701 0.2964234 0.00647029 0.000647029
2  0.2773723  0.2992701 0.2936496 0.01047051 0.001047051
3  0.2773723  0.2992701 0.2913139 0.01312701 0.001312701
4  0.2700730  0.2992701 0.2896350 0.01422057 0.001422057
5  0.2700730  0.2992701 0.2895620 0.01524962 0.001524962
6  0.2773723  0.2992701 0.2897810 0.01540569 0.001540569
7  0.2700730  0.2992701 0.2904380 0.01529332 0.001529332
8  0.2700730  0.3065693 0.2918978 0.01645286 0.001645286
9  0.2700730  0.3065693 0.2938686 0.01592513 0.001592513
10 0.2992701  0.3211679 0.2994891 0.01564677 0.001564677
11 0.3065693  0.3138686 0.3048905 0.01662727 0.001662727
12 0.3284672  0.3284672 0.3112409 0.01743819 0.001743819
13 0.3430657  0.3211679 0.3212409 0.01961606 0.001961606
14 0.3211679  0.3430657 0.3303650 0.02272090 0.002272090
15 0.3576642  0.3722628 0.3457664 0.02506426 0.002506426

$permut.pc.stepwise.lda$best.p
[1] 7

$permut.pc.stepwise.lda$best.error
[1] 0.2992701

$permut.pc.stepwise.lda$best.pda
$permut.pc.stepwise.lda$best.pda$class
  [1] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
 [19] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
 [37] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
 [55] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
 [73] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
 [91] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[109] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[127] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
Levels: CTL PHO

$permut.pc.stepwise.lda$best.pda$posterior
                CTL       PHO
YAL002W   0.6771091 0.3228909
YAL038W   0.7726007 0.2273993
YAR064W   0.5646115 0.4353885
YAR070C   0.7437130 0.2562870
YAR071W   0.8171349 0.1828651
YBL005W   0.6994080 0.3005920
YBL030C   0.7653499 0.2346501
YBR006W   0.7288392 0.2711608
YBR018C   0.7045617 0.2954383
YBR020W   0.8315812 0.1684188
YBR093C   0.8805387 0.1194613
YBR115C   0.8308869 0.1691131
YBR184W   0.7050854 0.2949146
YBR213W   0.7320570 0.2679430
YBR296C   0.7496786 0.2503214
YCL018W   0.6452265 0.3547735
YCR037C   0.6163044 0.3836956
YCR098C   0.6669545 0.3330455
YDL131W   0.7476162 0.2523838
YDL182W   0.7744471 0.2255529
YDL205C   0.6553470 0.3446530
YDL210W   0.7190080 0.2809920
YDR011W   0.7652571 0.2347429
YDR041W   0.5381432 0.4618568
YDR044W   0.8275864 0.1724136
YDR054C   0.6120761 0.3879239
YDR055W   0.5831320 0.4168680
YDR169C   0.5874476 0.4125524
YDR234W   0.6924355 0.3075645
YDR281C   0.7130679 0.2869321
YDR285W   0.6717936 0.3282064
YDR303C   0.6822923 0.3177077
YDR310C   0.5192697 0.4807303
YDR311W   0.6400275 0.3599725
YDR406W   0.7077033 0.2922967
YDR481C   0.7843271 0.2156729
YDR502C   0.7907487 0.2092513
YEL017C-A 0.5112395 0.4887605
YEL017W   0.5403898 0.4596102
YEL021W   0.6865641 0.3134359
YEL039C   0.6578841 0.3421159
YEL045C   0.5745393 0.4254607
YER017C   0.7501738 0.2498262
YER019W   0.7541783 0.2458217
YER026C   0.7043163 0.2956837
YER073W   0.5970823 0.4029177
YER086W   0.7237407 0.2762593
YER091C   0.6617745 0.3382255
YER179W   0.7648394 0.2351606
YFL004W   0.6072895 0.3927105
YFR030W   0.6814782 0.3185218
YGL009C   0.6566488 0.3433512
YGL073W   0.5953088 0.4046912
YGL213C   0.5147145 0.4852855
YGR019W   0.8071393 0.1928607
YGR044C   0.8289064 0.1710936
YGR088W   0.5719626 0.4280374
YGR121C   0.7377210 0.2622790
YGR157W   0.7851934 0.2148066
YGR233C   0.6469695 0.3530305
YGR281W   0.6038961 0.3961039
YHL022C   0.6971563 0.3028437
YHL036W   0.8128801 0.1871199
YHR007C   0.7069476 0.2930524
YHR008C   0.6718092 0.3281908
YHR014W   0.6123566 0.3876434
YHR037W   0.6323169 0.3676831
YHR136C   0.5916424 0.4083576
YHR137W   0.7006846 0.2993154
YHR153C   0.7053309 0.2946691
YHR168W   0.6561428 0.3438572
YHR215W   0.8673952 0.1326048
YIL015W   0.7483317 0.2516683
YIL046W   0.8702358 0.1297642
YIL072W   0.7828692 0.2171308
YIR017C   0.7188963 0.2811037
YIR034C   0.7272608 0.2727392
YJL012C   0.6008944 0.3991056
YJL106W   0.6028570 0.3971430
YJL117W   0.7777608 0.2222392
YJL153C   0.7903238 0.2096762
YJL209W   0.5994017 0.4005983
YJL211C   0.5406844 0.4593156
YJL219W   0.7919709 0.2080291
YJR010W   0.8401324 0.1598676
YJR048W   0.6826632 0.3173368
YJR073C   0.6126929 0.3873071
YJR094C   0.6205404 0.3794596
YJR137C   0.7282181 0.2717819
YJR152W   0.6855450 0.3144550
YKL001C   0.5643300 0.4356700
YKL182W   0.6795119 0.3204881
YKL216W   0.7666252 0.2333748
YKR039W   0.6973247 0.3026753
YKR048C   0.5097257 0.4902743
YKR050W   0.5931192 0.4068808
YKR069W   0.7623666 0.2376334
YLR081W   0.7296534 0.2703466
YLR142W   0.6849084 0.3150916
YLR180W   0.7871804 0.2128196
YLR263W   0.6757482 0.3242518
YLR303W   0.7323101 0.2676899
YLR329W   0.7163789 0.2836211
YLR420W   0.6912674 0.3087326
YLR438W   0.7731614 0.2268386
YML051W   0.6940272 0.3059728
YML054C   0.8788960 0.1211040
YML075C   0.7240144 0.2759856
YML121W   0.7446704 0.2553296
YML123C   0.8075099 0.1924901
YMR108W   0.6430644 0.3569356
YMR133W   0.7358631 0.2641369
YNL052W   0.6736964 0.3263036
YNL061W   0.8240303 0.1759697
YNL063W   0.5991427 0.4008573
YNL064C   0.6028533 0.3971467
YNL104C   0.7563501 0.2436499
YNL142W   0.6625248 0.3374752
YNL210W   0.6473045 0.3526955
YNL241C   0.7714828 0.2285172
YNL277W   0.7771936 0.2228064
YNR001C   0.7451779 0.2548221
YNR050C   0.8115453 0.1884547
YOL006C   0.5613183 0.4386817
YOR065W   0.7907803 0.2092197
YOR120W   0.7438563 0.2561437
YOR153W   0.6284147 0.3715853
YOR328W   0.7247741 0.2752259
YOR351C   0.7739294 0.2260706
YOR375C   0.8485913 0.1514087
YPL068C   0.7550181 0.2449819
YPL111W   0.7209572 0.2790428
YPL231W   0.6748330 0.3251670
YPR065W   0.6933749 0.3066251
YPR138C   0.6747081 0.3252919
YPR145W   0.7528976 0.2471024
YPR167C   0.6605959 0.3394041

$permut.pc.stepwise.lda$best.pda$call
lda(x = data.training, grouping = labels.training, CV = loo, 
    na.action = na.omit)

$permut.pc.stepwise.lda$best.pda$training.label
  [1] CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL PHO CTL PHO PHO CTL
 [19] CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL PHO PHO CTL
 [37] CTL CTL CTL CTL CTL CTL CTL CTL PHO PHO CTL CTL PHO CTL CTL CTL CTL CTL
 [55] CTL CTL CTL PHO PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL PHO
 [73] CTL PHO CTL CTL PHO PHO PHO CTL PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL
 [91] CTL CTL PHO CTL CTL PHO PHO CTL PHO CTL CTL CTL CTL PHO CTL PHO PHO CTL
[109] CTL CTL CTL PHO CTL CTL CTL PHO PHO PHO CTL CTL CTL PHO CTL CTL PHO PHO
[127] PHO PHO PHO CTL CTL CTL CTL CTL CTL CTL PHO
Levels: CTL PHO

$permut.pc.stepwise.lda$best.pda$pda.method
[1] "lda"

$permut.pc.stepwise.lda$best.pda$loo
[1] TRUE

$permut.pc.stepwise.lda$best.pda$validation
[1] "LOO"

$permut.pc.stepwise.lda$best.pda$confusion
      true
object CTL PHO
   CTL  96  41
   PHO   0   0
attr(,"error")
[1] 0.2992701



$stepwise.qda
$stepwise.qda$max.p
[1] 15

$stepwise.qda$errors
 [1] 0.08029197 0.04379562 0.03649635 0.05109489 0.07299270 0.08029197
 [7] 0.04379562 0.03649635 0.03649635 0.02919708 0.02919708 0.02919708
[13] 0.03649635 0.04379562 0.05109489

$stepwise.qda$confusion.table
   step              error added.var added.var.name CTL.CTL CTL.PHO PHO.CTL
1     1 0.0802919708029197         1        Pho4p.1      91       5       6
2     2 0.0437956204379562         8      Pho4p.t.2      93       3       3
3     3 0.0364963503649635        12        Met4p.3      94       2       3
4     4  0.051094890510949         5      Pho4p.g.2      92       4       3
5     5  0.072992700729927         6      Pho4p.g.3      91       5       5
6     6 0.0802919708029197         9      Pho4p.t.3      91       5       6
7     7 0.0437956204379562         2        Pho4p.2      92       4       2
8     8 0.0364963503649635         3        Pho4p.3      93       3       2
9     9 0.0364963503649635         4      Pho4p.g.1      93       3       2
10   10 0.0291970802919708        10        Met4p.1      94       2       2
11   11 0.0291970802919708        11        Met4p.2      94       2       2
12   12 0.0291970802919708         7      Pho4p.t.1      94       2       2
13   13 0.0364963503649635        14       Met31p.2      95       1       4
14   14 0.0437956204379562        15       Met31p.3      95       1       5
15   15  0.051094890510949        13       Met31p.1      95       1       6
   PHO.PHO
1       35
2       38
3       38
4       38
5       36
6       35
7       39
8       39
9       39
10      39
11      39
12      39
13      37
14      36
15      35

$stepwise.qda$best.pda
$stepwise.qda$best.pda$class
  [1] PHO CTL CTL PHO PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL PHO CTL PHO PHO
 [19] CTL CTL CTL CTL CTL PHO CTL PHO PHO PHO CTL PHO CTL PHO PHO PHO CTL CTL
 [37] CTL PHO PHO CTL CTL PHO PHO PHO CTL PHO CTL CTL CTL PHO CTL CTL CTL PHO
 [55] CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL PHO PHO CTL PHO PHO
 [73] CTL PHO CTL CTL CTL PHO CTL PHO CTL PHO PHO CTL CTL CTL CTL CTL CTL CTL
 [91] CTL CTL CTL CTL PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[109] PHO PHO CTL CTL CTL PHO PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[127] CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL
Levels: CTL PHO

$stepwise.qda$best.pda$posterior
                   CTL          PHO
YAL002W   3.130346e-05 9.999687e-01
YAL038W   7.584257e-01 2.415743e-01
YAR064W   1.000000e+00 3.889949e-10
YAR070C   1.127931e-10 1.000000e+00
YAR071W   3.811006e-06 9.999962e-01
YBL005W   1.000000e+00 7.591667e-20
YBL030C   1.000000e+00 2.277542e-23
YBR006W   1.000000e+00 8.787110e-19
YBR018C   1.000000e+00 9.709546e-17
YBR020W   1.000000e+00 6.999223e-26
YBR093C   8.150365e-09 1.000000e+00
YBR115C   1.000000e+00 1.260000e-27
YBR184W   1.000000e+00 2.650783e-18
YBR213W   1.000000e+00 3.024062e-10
YBR296C   1.663352e-09 1.000000e+00
YCL018W   1.000000e+00 5.702733e-20
YCR037C   1.972855e-11 1.000000e+00
YCR098C   1.346843e-05 9.999865e-01
YDL131W   1.000000e+00 1.213841e-14
YDL182W   1.000000e+00 1.679903e-12
YDL205C   1.000000e+00 1.403264e-21
YDL210W   1.000000e+00 3.157106e-13
YDR011W   1.000000e+00 2.719071e-15
YDR041W   4.266056e-05 9.999573e-01
YDR044W   1.000000e+00 1.561155e-26
YDR054C   4.682958e-04 9.995317e-01
YDR055W   8.973632e-04 9.991026e-01
YDR169C   1.067204e-06 9.999989e-01
YDR234W   1.000000e+00 6.677047e-14
YDR281C   1.840015e-05 9.999816e-01
YDR285W   1.000000e+00 6.860443e-25
YDR303C   1.170354e-04 9.998830e-01
YDR310C   1.518451e-09 1.000000e+00
YDR311W   3.258478e-09 1.000000e+00
YDR406W   1.000000e+00 2.042233e-21
YDR481C   9.960551e-01 3.944905e-03
YDR502C   1.000000e+00 3.490711e-13
YEL017C-A 1.412854e-03 9.985871e-01
YEL017W   4.252435e-04 9.995748e-01
YEL021W   1.000000e+00 7.336300e-30
YEL039C   1.000000e+00 3.143551e-23
YEL045C   2.585083e-01 7.414917e-01
YER017C   3.159045e-08 1.000000e+00
YER019W   3.159045e-08 1.000000e+00
YER026C   1.000000e+00 1.753445e-18
YER073W   3.709382e-03 9.962906e-01
YER086W   1.000000e+00 4.780029e-35
YER091C   1.000000e+00 8.823921e-20
YER179W   1.000000e+00 1.596102e-21
YFL004W   1.494391e-05 9.999851e-01
YFR030W   1.000000e+00 2.975097e-16
YGL009C   1.000000e+00 7.955653e-23
YGL073W   9.856246e-01 1.437536e-02
YGL213C   4.947316e-01 5.052684e-01
YGR019W   1.000000e+00 3.047100e-10
YGR044C   1.000000e+00 5.104846e-18
YGR088W   1.000000e+00 4.432716e-08
YGR121C   1.000000e+00 7.682255e-20
YGR157W   1.000000e+00 2.843339e-10
YGR233C   5.532491e-05 9.999447e-01
YGR281W   9.765398e-01 2.346016e-02
YHL022C   1.000000e+00 5.427731e-25
YHL036W   7.493916e-01 2.506084e-01
YHR007C   1.000000e+00 3.771024e-17
YHR008C   1.000000e+00 4.602213e-15
YHR014W   1.000000e+00 3.145576e-12
YHR037W   9.999993e-01 6.517486e-07
YHR136C   1.690963e-03 9.983090e-01
YHR137W   1.468716e-03 9.985313e-01
YHR153C   1.000000e+00 2.535472e-08
YHR168W   2.049603e-11 1.000000e+00
YHR215W   3.811006e-06 9.999962e-01
YIL015W   1.000000e+00 1.661960e-20
YIL046W   7.633862e-03 9.923661e-01
YIL072W   1.000000e+00 6.955819e-22
YIR017C   1.000000e+00 1.328751e-11
YIR034C   9.938091e-01 6.190880e-03
YJL012C   6.028621e-06 9.999940e-01
YJL106W   1.000000e+00 6.938636e-11
YJL117W   4.762713e-02 9.523729e-01
YJL153C   1.000000e+00 2.401171e-20
YJL209W   9.715107e-09 1.000000e+00
YJL211C   9.715107e-09 1.000000e+00
YJL219W   1.000000e+00 9.900535e-13
YJR010W   1.000000e+00 2.639687e-35
YJR048W   1.000000e+00 6.999772e-17
YJR073C   9.528718e-01 4.712824e-02
YJR094C   1.000000e+00 1.203937e-08
YJR137C   1.000000e+00 3.787560e-20
YJR152W   1.000000e+00 3.052164e-20
YKL001C   1.000000e+00 3.396681e-08
YKL182W   1.000000e+00 2.236184e-19
YKL216W   1.000000e+00 4.879548e-21
YKR039W   1.000000e+00 3.835179e-22
YKR048C   6.888719e-06 9.999931e-01
YKR050W   6.771113e-06 9.999932e-01
YKR069W   5.642212e-01 4.357788e-01
YLR081W   1.000000e+00 4.701130e-21
YLR142W   1.000000e+00 3.397916e-13
YLR180W   1.000000e+00 2.917203e-08
YLR263W   1.000000e+00 3.221399e-27
YLR303W   1.000000e+00 4.088260e-17
YLR329W   1.000000e+00 7.157323e-12
YLR420W   1.000000e+00 2.862772e-14
YLR438W   1.000000e+00 1.393311e-10
YML051W   1.000000e+00 4.557210e-22
YML054C   1.000000e+00 1.696385e-08
YML075C   1.000000e+00 2.910558e-15
YML121W   1.002097e-02 9.899790e-01
YML123C   4.030584e-09 1.000000e+00
YMR108W   1.000000e+00 1.245857e-12
YMR133W   1.000000e+00 2.169844e-29
YNL052W   1.000000e+00 1.105096e-14
YNL061W   3.709901e-08 1.000000e+00
YNL063W   4.620964e-03 9.953790e-01
YNL064C   4.341213e-03 9.956588e-01
YNL104C   9.170441e-01 8.295595e-02
YNL142W   1.000000e+00 1.652858e-21
YNL210W   1.000000e+00 5.638027e-20
YNL241C   1.000000e+00 2.978388e-11
YNL277W   1.000000e+00 2.100774e-29
YNR001C   1.000000e+00 6.216555e-22
YNR050C   9.999995e-01 4.694420e-07
YOL006C   1.000000e+00 1.137870e-08
YOR065W   9.999998e-01 1.890801e-07
YOR120W   1.000000e+00 4.412612e-17
YOR153W   1.000000e+00 1.012873e-09
YOR328W   1.000000e+00 1.099435e-15
YOR351C   1.000000e+00 1.588203e-23
YOR375C   1.000000e+00 3.914672e-17
YPL068C   2.120237e-05 9.999788e-01
YPL111W   1.000000e+00 3.570552e-17
YPL231W   1.000000e+00 2.135727e-08
YPR065W   1.000000e+00 5.190173e-13
YPR138C   1.000000e+00 3.433133e-23
YPR145W   1.000000e+00 6.550178e-11
YPR167C   9.999999e-01 5.084353e-08

$stepwise.qda$best.pda$call
qda(x = data.training, grouping = labels.training, CV = loo, 
    na.action = na.omit)

$stepwise.qda$best.pda$training.names
  [1] "YAL002W"   "YAL038W"   "YAR064W"   "YAR070C"   "YAR071W"   "YBL005W"  
  [7] "YBL030C"   "YBR006W"   "YBR018C"   "YBR020W"   "YBR093C"   "YBR115C"  
 [13] "YBR184W"   "YBR213W"   "YBR296C"   "YCL018W"   "YCR037C"   "YCR098C"  
 [19] "YDL131W"   "YDL182W"   "YDL205C"   "YDL210W"   "YDR011W"   "YDR041W"  
 [25] "YDR044W"   "YDR054C"   "YDR055W"   "YDR169C"   "YDR234W"   "YDR281C"  
 [31] "YDR285W"   "YDR303C"   "YDR310C"   "YDR311W"   "YDR406W"   "YDR481C"  
 [37] "YDR502C"   "YEL017C-A" "YEL017W"   "YEL021W"   "YEL039C"   "YEL045C"  
 [43] "YER017C"   "YER019W"   "YER026C"   "YER073W"   "YER086W"   "YER091C"  
 [49] "YER179W"   "YFL004W"   "YFR030W"   "YGL009C"   "YGL073W"   "YGL213C"  
 [55] "YGR019W"   "YGR044C"   "YGR088W"   "YGR121C"   "YGR157W"   "YGR233C"  
 [61] "YGR281W"   "YHL022C"   "YHL036W"   "YHR007C"   "YHR008C"   "YHR014W"  
 [67] "YHR037W"   "YHR136C"   "YHR137W"   "YHR153C"   "YHR168W"   "YHR215W"  
 [73] "YIL015W"   "YIL046W"   "YIL072W"   "YIR017C"   "YIR034C"   "YJL012C"  
 [79] "YJL106W"   "YJL117W"   "YJL153C"   "YJL209W"   "YJL211C"   "YJL219W"  
 [85] "YJR010W"   "YJR048W"   "YJR073C"   "YJR094C"   "YJR137C"   "YJR152W"  
 [91] "YKL001C"   "YKL182W"   "YKL216W"   "YKR039W"   "YKR048C"   "YKR050W"  
 [97] "YKR069W"   "YLR081W"   "YLR142W"   "YLR180W"   "YLR263W"   "YLR303W"  
[103] "YLR329W"   "YLR420W"   "YLR438W"   "YML051W"   "YML054C"   "YML075C"  
[109] "YML121W"   "YML123C"   "YMR108W"   "YMR133W"   "YNL052W"   "YNL061W"  
[115] "YNL063W"   "YNL064C"   "YNL104C"   "YNL142W"   "YNL210W"   "YNL241C"  
[121] "YNL277W"   "YNR001C"   "YNR050C"   "YOL006C"   "YOR065W"   "YOR120W"  
[127] "YOR153W"   "YOR328W"   "YOR351C"   "YOR375C"   "YPL068C"   "YPL111W"  
[133] "YPL231W"   "YPR065W"   "YPR138C"   "YPR145W"   "YPR167C"  

$stepwise.qda$best.pda$training.label
  [1] PHO CTL PHO PHO PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL PHO CTL PHO PHO
 [19] CTL CTL CTL CTL CTL PHO CTL PHO PHO PHO CTL PHO CTL PHO PHO PHO CTL PHO
 [37] CTL PHO PHO CTL CTL PHO PHO PHO CTL PHO CTL CTL CTL PHO CTL CTL CTL CTL
 [55] CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL PHO PHO CTL PHO PHO
 [73] CTL CTL CTL CTL CTL PHO CTL PHO CTL PHO PHO CTL CTL CTL CTL CTL CTL CTL
 [91] CTL CTL CTL CTL PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[109] PHO PHO CTL CTL CTL PHO PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[127] CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL
Levels: CTL PHO

$stepwise.qda$best.pda$pda.method
[1] "qda"

$stepwise.qda$best.pda$loo
[1] TRUE

$stepwise.qda$best.pda$validation
[1] "LOO"

$stepwise.qda$best.pda$confusion
      true
object CTL PHO
   CTL  94   2
   PHO   2  39
attr(,"error")
[1] 0.02919708


$stepwise.qda$best.p
[1] 12

$stepwise.qda$best.vars
 [1]  1  8 12  5  6  9  2  3  4 10 11  7

$stepwise.qda$best.var.names
 [1] "Pho4p.1"   "Pho4p.t.2" "Met4p.3"   "Pho4p.g.2" "Pho4p.g.3" "Pho4p.t.3"
 [7] "Pho4p.2"   "Pho4p.3"   "Pho4p.g.1" "Met4p.1"   "Met4p.2"   "Pho4p.t.1"

$stepwise.qda$best.error
[1] 0.02919708

$stepwise.qda$pc.transform
[1] FALSE

$stepwise.qda$var.order
 [1]  1  8 12  5  6  9  2  3  4 10 11  7 14 15 13


$pc.stepwise.qda
$pc.stepwise.qda$max.p
[1] 15

$pc.stepwise.qda$errors
 [1] 0.12408759 0.07299270 0.04379562 0.03649635 0.03649635 0.05839416
 [7] 0.06569343 0.04379562 0.04379562 0.03649635 0.03649635 0.03649635
[13] 0.05839416 0.05109489 0.05109489

$pc.stepwise.qda$confusion.table
   step              error added.var added.var.name CTL.CTL CTL.PHO PHO.CTL
1     1  0.124087591240876         1         Comp.1      87       9       8
2     2  0.072992700729927         5         Comp.5      89       7       3
3     3 0.0437956204379562         2         Comp.2      92       4       2
4     4 0.0364963503649635         3         Comp.3      92       4       1
5     5 0.0364963503649635         7         Comp.7      92       4       1
6     6 0.0583941605839416         9         Comp.9      91       5       3
7     7 0.0656934306569343        11        Comp.11      90       6       3
8     8 0.0437956204379562        15        Comp.15      92       4       2
9     9 0.0437956204379562        12        Comp.12      92       4       2
10   10 0.0364963503649635         6         Comp.6      94       2       3
11   11 0.0364963503649635        10        Comp.10      94       2       3
12   12 0.0364963503649635        14        Comp.14      94       2       3
13   13 0.0583941605839416        13        Comp.13      93       3       5
14   14  0.051094890510949         8         Comp.8      95       1       6
15   15  0.051094890510949         4         Comp.4      95       1       6
   PHO.PHO
1       33
2       38
3       39
4       40
5       40
6       38
7       38
8       39
9       39
10      38
11      38
12      38
13      36
14      35
15      35

$pc.stepwise.qda$best.pda
$pc.stepwise.qda$best.pda$class
  [1] PHO CTL PHO PHO PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL PHO CTL PHO PHO
 [19] CTL CTL CTL CTL CTL PHO CTL PHO PHO PHO CTL PHO CTL PHO PHO PHO CTL CTL
 [37] CTL PHO PHO CTL CTL PHO PHO PHO CTL PHO CTL CTL CTL PHO CTL CTL CTL PHO
 [55] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO PHO CTL PHO PHO
 [73] CTL PHO CTL CTL CTL PHO CTL CTL CTL PHO PHO CTL CTL CTL CTL CTL CTL CTL
 [91] CTL CTL CTL CTL PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[109] PHO PHO CTL CTL CTL PHO PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[127] CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL
Levels: CTL PHO

$pc.stepwise.qda$best.pda$posterior
                   CTL          PHO
YAL002W   2.759092e-05 9.999724e-01
YAL038W   9.979380e-01 2.062028e-03
YAR064W   1.564097e-01 8.435903e-01
YAR070C   4.718168e-07 9.999995e-01
YAR071W   5.550155e-06 9.999944e-01
YBL005W   1.000000e+00 4.828546e-15
YBL030C   1.000000e+00 2.642063e-18
YBR006W   1.000000e+00 1.891876e-10
YBR018C   1.000000e+00 1.458456e-13
YBR020W   1.000000e+00 1.160450e-14
YBR093C   6.119985e-09 1.000000e+00
YBR115C   1.000000e+00 1.912108e-19
YBR184W   1.000000e+00 1.327605e-15
YBR213W   1.000000e+00 6.036761e-13
YBR296C   7.815728e-10 1.000000e+00
YCL018W   1.000000e+00 4.552504e-16
YCR037C   1.231266e-06 9.999988e-01
YCR098C   1.676598e-04 9.998323e-01
YDL131W   1.000000e+00 1.799193e-11
YDL182W   1.000000e+00 1.769863e-11
YDL205C   1.000000e+00 8.416256e-21
YDL210W   1.000000e+00 1.790961e-12
YDR011W   1.000000e+00 2.495232e-12
YDR041W   2.845024e-04 9.997155e-01
YDR044W   1.000000e+00 8.702956e-20
YDR054C   3.733172e-03 9.962668e-01
YDR055W   4.340284e-04 9.995660e-01
YDR169C   4.257095e-09 1.000000e+00
YDR234W   1.000000e+00 1.942887e-09
YDR281C   7.367464e-06 9.999926e-01
YDR285W   1.000000e+00 6.481483e-21
YDR303C   7.112316e-03 9.928877e-01
YDR310C   7.084124e-08 9.999999e-01
YDR311W   3.542143e-08 1.000000e+00
YDR406W   1.000000e+00 5.574869e-23
YDR481C   9.986760e-01 1.324048e-03
YDR502C   1.000000e+00 4.375728e-12
YEL017C-A 4.607675e-05 9.999539e-01
YEL017W   3.161782e-04 9.996838e-01
YEL021W   1.000000e+00 8.010793e-22
YEL039C   1.000000e+00 5.507851e-19
YEL045C   3.027922e-02 9.697208e-01
YER017C   4.191813e-06 9.999958e-01
YER019W   5.040325e-06 9.999950e-01
YER026C   1.000000e+00 9.494889e-13
YER073W   8.677404e-05 9.999132e-01
YER086W   1.000000e+00 3.375860e-26
YER091C   1.000000e+00 1.795500e-17
YER179W   1.000000e+00 7.691938e-15
YFL004W   7.625060e-06 9.999924e-01
YFR030W   1.000000e+00 1.467611e-11
YGL009C   1.000000e+00 9.022376e-21
YGL073W   7.668085e-01 2.331915e-01
YGL213C   1.551342e-01 8.448658e-01
YGR019W   1.000000e+00 3.594173e-11
YGR044C   1.000000e+00 1.383397e-15
YGR088W   9.999997e-01 3.487719e-07
YGR121C   1.000000e+00 5.963920e-16
YGR157W   1.000000e+00 4.245419e-16
YGR233C   9.920338e-01 7.966168e-03
YGR281W   9.999945e-01 5.450451e-06
YHL022C   1.000000e+00 1.344748e-18
YHL036W   9.999981e-01 1.886017e-06
YHR007C   1.000000e+00 2.833757e-10
YHR008C   1.000000e+00 7.478468e-11
YHR014W   1.000000e+00 3.034273e-11
YHR037W   9.999772e-01 2.275067e-05
YHR136C   3.288407e-06 9.999967e-01
YHR137W   1.921886e-06 9.999981e-01
YHR153C   9.999985e-01 1.514048e-06
YHR168W   6.911035e-12 1.000000e+00
YHR215W   5.550155e-06 9.999944e-01
YIL015W   1.000000e+00 1.772210e-14
YIL046W   4.040680e-01 5.959320e-01
YIL072W   1.000000e+00 1.830929e-13
YIR017C   1.000000e+00 2.779390e-10
YIR034C   9.920034e-01 7.996594e-03
YJL012C   2.450057e-06 9.999975e-01
YJL106W   1.000000e+00 1.255950e-11
YJL117W   8.798667e-01 1.201333e-01
YJL153C   1.000000e+00 1.800402e-16
YJL209W   1.854349e-06 9.999981e-01
YJL211C   1.854349e-06 9.999981e-01
YJL219W   1.000000e+00 3.025181e-08
YJR010W   1.000000e+00 2.445312e-12
YJR048W   1.000000e+00 1.400965e-10
YJR073C   9.271549e-01 7.284513e-02
YJR094C   1.000000e+00 8.779041e-10
YJR137C   1.000000e+00 6.874165e-14
YJR152W   1.000000e+00 1.652912e-11
YKL001C   1.000000e+00 2.968780e-12
YKL182W   1.000000e+00 3.583028e-15
YKL216W   1.000000e+00 8.682292e-15
YKR039W   1.000000e+00 3.615515e-20
YKR048C   2.627571e-05 9.999737e-01
YKR050W   2.669914e-05 9.999733e-01
YKR069W   8.794904e-01 1.205096e-01
YLR081W   1.000000e+00 2.087767e-13
YLR142W   1.000000e+00 1.676606e-11
YLR180W   1.000000e+00 1.366872e-08
YLR263W   1.000000e+00 1.714536e-23
YLR303W   1.000000e+00 3.265435e-14
YLR329W   1.000000e+00 6.411126e-12
YLR420W   1.000000e+00 2.752570e-15
YLR438W   1.000000e+00 2.247246e-08
YML051W   1.000000e+00 3.714658e-19
YML054C   9.999798e-01 2.016627e-05
YML075C   1.000000e+00 3.804257e-16
YML121W   1.399230e-04 9.998601e-01
YML123C   1.753936e-08 1.000000e+00
YMR108W   1.000000e+00 7.822720e-16
YMR133W   1.000000e+00 1.016777e-22
YNL052W   1.000000e+00 2.176934e-13
YNL061W   4.427949e-01 5.572051e-01
YNL063W   9.264930e-05 9.999074e-01
YNL064C   7.130357e-05 9.999287e-01
YNL104C   9.999917e-01 8.349936e-06
YNL142W   1.000000e+00 2.658922e-23
YNL210W   1.000000e+00 8.041216e-16
YNL241C   1.000000e+00 2.594484e-08
YNL277W   1.000000e+00 1.416386e-19
YNR001C   1.000000e+00 1.196156e-18
YNR050C   9.999994e-01 5.957287e-07
YOL006C   1.000000e+00 4.940306e-10
YOR065W   9.999984e-01 1.638069e-06
YOR120W   1.000000e+00 3.743128e-15
YOR153W   1.000000e+00 3.570814e-09
YOR328W   1.000000e+00 2.192677e-11
YOR351C   1.000000e+00 4.233852e-17
YOR375C   1.000000e+00 4.741724e-14
YPL068C   5.070795e-08 9.999999e-01
YPL111W   1.000000e+00 7.907091e-14
YPL231W   9.998483e-01 1.517030e-04
YPR065W   1.000000e+00 4.135889e-12
YPR138C   1.000000e+00 4.054183e-19
YPR145W   1.000000e+00 1.983135e-10
YPR167C   1.000000e+00 8.276084e-09

$pc.stepwise.qda$best.pda$call
qda(x = data.training, grouping = labels.training, CV = loo, 
    na.action = na.omit)

$pc.stepwise.qda$best.pda$training.names
  [1] "YAL002W"   "YAL038W"   "YAR064W"   "YAR070C"   "YAR071W"   "YBL005W"  
  [7] "YBL030C"   "YBR006W"   "YBR018C"   "YBR020W"   "YBR093C"   "YBR115C"  
 [13] "YBR184W"   "YBR213W"   "YBR296C"   "YCL018W"   "YCR037C"   "YCR098C"  
 [19] "YDL131W"   "YDL182W"   "YDL205C"   "YDL210W"   "YDR011W"   "YDR041W"  
 [25] "YDR044W"   "YDR054C"   "YDR055W"   "YDR169C"   "YDR234W"   "YDR281C"  
 [31] "YDR285W"   "YDR303C"   "YDR310C"   "YDR311W"   "YDR406W"   "YDR481C"  
 [37] "YDR502C"   "YEL017C-A" "YEL017W"   "YEL021W"   "YEL039C"   "YEL045C"  
 [43] "YER017C"   "YER019W"   "YER026C"   "YER073W"   "YER086W"   "YER091C"  
 [49] "YER179W"   "YFL004W"   "YFR030W"   "YGL009C"   "YGL073W"   "YGL213C"  
 [55] "YGR019W"   "YGR044C"   "YGR088W"   "YGR121C"   "YGR157W"   "YGR233C"  
 [61] "YGR281W"   "YHL022C"   "YHL036W"   "YHR007C"   "YHR008C"   "YHR014W"  
 [67] "YHR037W"   "YHR136C"   "YHR137W"   "YHR153C"   "YHR168W"   "YHR215W"  
 [73] "YIL015W"   "YIL046W"   "YIL072W"   "YIR017C"   "YIR034C"   "YJL012C"  
 [79] "YJL106W"   "YJL117W"   "YJL153C"   "YJL209W"   "YJL211C"   "YJL219W"  
 [85] "YJR010W"   "YJR048W"   "YJR073C"   "YJR094C"   "YJR137C"   "YJR152W"  
 [91] "YKL001C"   "YKL182W"   "YKL216W"   "YKR039W"   "YKR048C"   "YKR050W"  
 [97] "YKR069W"   "YLR081W"   "YLR142W"   "YLR180W"   "YLR263W"   "YLR303W"  
[103] "YLR329W"   "YLR420W"   "YLR438W"   "YML051W"   "YML054C"   "YML075C"  
[109] "YML121W"   "YML123C"   "YMR108W"   "YMR133W"   "YNL052W"   "YNL061W"  
[115] "YNL063W"   "YNL064C"   "YNL104C"   "YNL142W"   "YNL210W"   "YNL241C"  
[121] "YNL277W"   "YNR001C"   "YNR050C"   "YOL006C"   "YOR065W"   "YOR120W"  
[127] "YOR153W"   "YOR328W"   "YOR351C"   "YOR375C"   "YPL068C"   "YPL111W"  
[133] "YPL231W"   "YPR065W"   "YPR138C"   "YPR145W"   "YPR167C"  

$pc.stepwise.qda$best.pda$training.label
  [1] PHO CTL PHO PHO PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL PHO CTL PHO PHO
 [19] CTL CTL CTL CTL CTL PHO CTL PHO PHO PHO CTL PHO CTL PHO PHO PHO CTL PHO
 [37] CTL PHO PHO CTL CTL PHO PHO PHO CTL PHO CTL CTL CTL PHO CTL CTL CTL CTL
 [55] CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL PHO PHO CTL PHO PHO
 [73] CTL CTL CTL CTL CTL PHO CTL PHO CTL PHO PHO CTL CTL CTL CTL CTL CTL CTL
 [91] CTL CTL CTL CTL PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[109] PHO PHO CTL CTL CTL PHO PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[127] CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL
Levels: CTL PHO

$pc.stepwise.qda$best.pda$pda.method
[1] "qda"

$pc.stepwise.qda$best.pda$loo
[1] TRUE

$pc.stepwise.qda$best.pda$validation
[1] "LOO"

$pc.stepwise.qda$best.pda$confusion
      true
object CTL PHO
   CTL  94   3
   PHO   2  38
attr(,"error")
[1] 0.03649635


$pc.stepwise.qda$best.p
[1] 12

$pc.stepwise.qda$best.vars
 [1]  1  5  2  3  7  9 11 15 12  6 10 14

$pc.stepwise.qda$best.var.names
 [1] "Comp.1"  "Comp.5"  "Comp.2"  "Comp.3"  "Comp.7"  "Comp.9"  "Comp.11"
 [8] "Comp.15" "Comp.12" "Comp.6"  "Comp.10" "Comp.14"

$pc.stepwise.qda$best.error
[1] 0.03649635

$pc.stepwise.qda$pc.transform
[1] TRUE

$pc.stepwise.qda$var.order
 [1]  1  5  2  3  7  9 11 15 12  6 10 14 13  8  4


$permut.stepwise.qda
$permut.stepwise.qda$confusion.table
        error CTL.CTL CTL.PHO PHO.CTL PHO.PHO
1   0.2773723      96       0      38       3
2   0.3065693      95       1      41       0
3   0.2992701      96       0      41       0
4   0.2992701      92       4      37       4
5   0.3065693      88       8      34       7
6   0.2919708      91       5      35       6
7   0.2992701      96       0      41       0
8   0.2992701      96       0      41       0
9   0.2992701      96       0      41       0
10  0.2992701      96       0      41       0
11  0.2992701      86      10      31      10
12  0.2992701      96       0      41       0
13  0.2992701      96       0      41       0
14  0.2992701      96       0      41       0
15  0.2992701      96       0      41       0
16  0.2992701      91       5      36       5
17  0.2992701      93       3      38       3
18  0.2700730      92       4      33       8
19  0.2627737      96       0      36       5
20  0.2992701      96       0      41       0
21  0.2992701      96       0      41       0
22  0.2554745      93       3      32       9
23  0.2992701      96       0      41       0
24  0.2992701      96       0      41       0
25  0.2992701      92       4      37       4
26  0.2992701      96       0      41       0
27  0.2992701      96       0      41       0
28  0.2992701      96       0      41       0
29  0.2992701      96       0      41       0
30  0.2992701      96       0      41       0
31  0.3065693      95       1      41       0
32  0.2992701      96       0      41       0
33  0.2992701      96       0      41       0
34  0.2846715      87       9      30      11
35  0.2992701      96       0      41       0
36  0.2700730      89       7      30      11
37  0.2700730      87       9      28      13
38  0.2992701      96       0      41       0
39  0.2919708      92       4      36       5
40  0.2919708      94       2      38       3
41  0.2846715      92       4      35       6
42  0.2919708      89       7      33       8
43  0.2992701      96       0      41       0
44  0.2992701      96       0      41       0
45  0.2992701      96       0      41       0
46  0.2992701      96       0      41       0
47  0.2992701      83      13      28      13
48  0.2919708      93       3      37       4
49  0.2919708      90       6      34       7
50  0.2992701      93       3      38       3
51  0.2992701      96       0      41       0
52  0.2992701      96       0      41       0
53  0.2992701      81      15      26      15
54  0.3065693      91       5      37       4
55  0.2773723      84      12      26      15
56  0.3138686      92       4      39       2
57  0.2919708      88       8      32       9
58  0.2992701      96       0      41       0
59  0.2992701      96       0      41       0
60  0.2992701      96       0      41       0
61  0.2992701      96       0      41       0
62  0.2992701      96       0      41       0
63  0.2846715      91       5      34       7
64  0.2992701      96       0      41       0
65  0.2554745      82      14      21      20
66  0.2481752      93       3      31      10
67  0.2992701      96       0      41       0
68  0.2992701      96       0      41       0
69  0.2700730      92       4      33       8
70  0.2992701      96       0      41       0
71  0.2992701      96       0      41       0
72  0.2627737      90       6      30      11
73  0.2992701      96       0      41       0
74  0.2992701      96       0      41       0
75  0.2992701      93       3      38       3
76  0.3138686      93       3      40       1
77  0.2992701      96       0      41       0
78  0.3065693      90       6      36       5
79  0.2992701      96       0      41       0
80  0.2992701      96       0      41       0
81  0.2627737      84      12      24      17
82  0.2919708      91       5      35       6
83  0.2992701      96       0      41       0
84  0.2992701      85      11      30      11
85  0.2992701      96       0      41       0
86  0.2992701      96       0      41       0
87  0.2408759      93       3      30      11
88  0.2992701      96       0      41       0
89  0.2992701      96       0      41       0
90  0.2700730      92       4      33       8
91  0.2992701      91       5      36       5
92  0.2992701      96       0      41       0
93  0.2992701      96       0      41       0
94  0.2627737      88       8      28      13
95  0.2992701      96       0      41       0
96  0.2992701      96       0      41       0
97  0.2700730      87       9      28      13
98  0.2773723      90       6      32       9
99  0.2992701      96       0      41       0
100 0.2773723      91       5      33       8

$permut.stepwise.qda$errors
    permut.1  permut.2  permut.3  permut.4  permut.5  permut.6  permut.7
1  0.2773723 0.3065693 0.2992701 0.2992701 0.3211679 0.2992701 0.2992701
2  0.3357664 0.3284672 0.2992701 0.3211679 0.3065693 0.2992701 0.2992701
3  0.3138686 0.3284672 0.3284672 0.2992701 0.3211679 0.2992701 0.3138686
4  0.3357664 0.3649635 0.3284672 0.3138686 0.3138686 0.2919708 0.3065693
5  0.3430657 0.3649635 0.3649635 0.3357664 0.3211679 0.3649635 0.3430657
6  0.3649635 0.3795620 0.4233577 0.3795620 0.3357664 0.3430657 0.3138686
7  0.3795620 0.3576642 0.4014599 0.4598540 0.3357664 0.3357664 0.3430657
8  0.3649635 0.3795620 0.4452555 0.4452555 0.3430657 0.4306569 0.3649635
9  0.3576642 0.3941606 0.4306569 0.4598540 0.3795620 0.4233577 0.3649635
10 0.4306569 0.4452555 0.4306569 0.4671533 0.3868613 0.3941606 0.3503650
11 0.3649635 0.4379562 0.3649635 0.4014599 0.3868613 0.4014599 0.3795620
12 0.3284672 0.4379562 0.3211679 0.3503650 0.3649635 0.4525547 0.3357664
13 0.3430657 0.4525547 0.3503650 0.3211679 0.3722628 0.4160584 0.3576642
14 0.3430657 0.4306569 0.3503650 0.3649635 0.3503650 0.4014599 0.3722628
15 0.3503650 0.4379562 0.3649635 0.3576642 0.3649635 0.4014599 0.3649635
    permut.8  permut.9 permut.10 permut.11 permut.12 permut.13 permut.14
1  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
2  0.3065693 0.3065693 0.3211679 0.3211679 0.3138686 0.3065693 0.3284672
3  0.3284672 0.3430657 0.3138686 0.3430657 0.3211679 0.3138686 0.3284672
4  0.3576642 0.3065693 0.3284672 0.3065693 0.3503650 0.3357664 0.3211679
5  0.3795620 0.3430657 0.3357664 0.2992701 0.3722628 0.3357664 0.3430657
6  0.3649635 0.3430657 0.4014599 0.3284672 0.3795620 0.4306569 0.3503650
7  0.4014599 0.3649635 0.3722628 0.3284672 0.4160584 0.4379562 0.3503650
8  0.4014599 0.3868613 0.3941606 0.3430657 0.4014599 0.4379562 0.3722628
9  0.3357664 0.3722628 0.4087591 0.3795620 0.4087591 0.4525547 0.3795620
10 0.3576642 0.3868613 0.4379562 0.4306569 0.3941606 0.4671533 0.3941606
11 0.3722628 0.3941606 0.4306569 0.4233577 0.3576642 0.4233577 0.4014599
12 0.3868613 0.4014599 0.3868613 0.4379562 0.3576642 0.4087591 0.4233577
13 0.3868613 0.4087591 0.4014599 0.4306569 0.3503650 0.4087591 0.4452555
14 0.3284672 0.3868613 0.3941606 0.4087591 0.3649635 0.4379562 0.4233577
15 0.4014599 0.3941606 0.3941606 0.4014599 0.3722628 0.3868613 0.4379562
   permut.15 permut.16 permut.17 permut.18 permut.19 permut.20 permut.21
1  0.2992701 0.2992701 0.2992701 0.2846715 0.2992701 0.2992701 0.2992701
2  0.3211679 0.3065693 0.2992701 0.2700730 0.2992701 0.2992701 0.3065693
3  0.3357664 0.2992701 0.3284672 0.2773723 0.2992701 0.3357664 0.3430657
4  0.3576642 0.3284672 0.4014599 0.2846715 0.2627737 0.3430657 0.3430657
5  0.3649635 0.3138686 0.3649635 0.2919708 0.3211679 0.3795620 0.3941606
6  0.3357664 0.3503650 0.3649635 0.3065693 0.3430657 0.3941606 0.3795620
7  0.3649635 0.3576642 0.4014599 0.3576642 0.3795620 0.4379562 0.3868613
8  0.3795620 0.3430657 0.4379562 0.3795620 0.4014599 0.4598540 0.4233577
9  0.3503650 0.3649635 0.4452555 0.3576642 0.4233577 0.4087591 0.3795620
10 0.3795620 0.3503650 0.4379562 0.4014599 0.4379562 0.4014599 0.4160584
11 0.3576642 0.3795620 0.4306569 0.4233577 0.4817518 0.4233577 0.3941606
12 0.3722628 0.4160584 0.4014599 0.4160584 0.4379562 0.4598540 0.3649635
13 0.3649635 0.4306569 0.4087591 0.4160584 0.4379562 0.4671533 0.3649635
14 0.3795620 0.4087591 0.3649635 0.4452555 0.4379562 0.4160584 0.3722628
15 0.3941606 0.4525547 0.4233577 0.4087591 0.4452555 0.4233577 0.3722628
   permut.22 permut.23 permut.24 permut.25 permut.26 permut.27 permut.28
1  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
2  0.2554745 0.2992701 0.2992701 0.2992701 0.3065693 0.3138686 0.3138686
3  0.2700730 0.3065693 0.2992701 0.3138686 0.3430657 0.3138686 0.3795620
4  0.3065693 0.3284672 0.3430657 0.3576642 0.3357664 0.3065693 0.3795620
5  0.3065693 0.3503650 0.3795620 0.3138686 0.3503650 0.3430657 0.3868613
6  0.3868613 0.3722628 0.3649635 0.3649635 0.3576642 0.3430657 0.3868613
7  0.2992701 0.3722628 0.4233577 0.3576642 0.3941606 0.3503650 0.3722628
8  0.2992701 0.3941606 0.4087591 0.4306569 0.4671533 0.3357664 0.3795620
9  0.3211679 0.3795620 0.4014599 0.4233577 0.4671533 0.4087591 0.3941606
10 0.3284672 0.3941606 0.4525547 0.4379562 0.4963504 0.4160584 0.4014599
11 0.3138686 0.4233577 0.4963504 0.4452555 0.4890511 0.3722628 0.4525547
12 0.3284672 0.4160584 0.4963504 0.4233577 0.4160584 0.3795620 0.4525547
13 0.3138686 0.4160584 0.4963504 0.4452555 0.4233577 0.3868613 0.4890511
14 0.3211679 0.3868613 0.4890511 0.3941606 0.4014599 0.3357664 0.4598540
15 0.3576642 0.4014599 0.4963504 0.3941606 0.4014599 0.3138686 0.4452555
   permut.29 permut.30 permut.31 permut.32 permut.33 permut.34 permut.35
1  0.2992701 0.2992701 0.3065693 0.2992701 0.2992701 0.3284672 0.2992701
2  0.3211679 0.2992701 0.3503650 0.2992701 0.2992701 0.3138686 0.3138686
3  0.3649635 0.3211679 0.3722628 0.3065693 0.3211679 0.3284672 0.3284672
4  0.3284672 0.3138686 0.3868613 0.3138686 0.3649635 0.3065693 0.3503650
5  0.3503650 0.3357664 0.3649635 0.3722628 0.3503650 0.2846715 0.3576642
6  0.3576642 0.3576642 0.4014599 0.3284672 0.4087591 0.3065693 0.4233577
7  0.3941606 0.3868613 0.3941606 0.3284672 0.3941606 0.3284672 0.4379562
8  0.4087591 0.4014599 0.3430657 0.3357664 0.4379562 0.3503650 0.4817518
9  0.3795620 0.4671533 0.3357664 0.4014599 0.4817518 0.3357664 0.4306569
10 0.4087591 0.5036496 0.3211679 0.3941606 0.4452555 0.3649635 0.4452555
11 0.4014599 0.5036496 0.3430657 0.3868613 0.4014599 0.3138686 0.4671533
12 0.4160584 0.4598540 0.3722628 0.3649635 0.3722628 0.3211679 0.4525547
13 0.4014599 0.4452555 0.3503650 0.3649635 0.3795620 0.3357664 0.4452555
14 0.4014599 0.4452555 0.3430657 0.3722628 0.4014599 0.3211679 0.4306569
15 0.3722628 0.3868613 0.3430657 0.3795620 0.3941606 0.3576642 0.4671533
   permut.36 permut.37 permut.38 permut.39 permut.40 permut.41 permut.42
1  0.2919708 0.2773723 0.2992701 0.2992701 0.2992701 0.2992701 0.3065693
2  0.2700730 0.2846715 0.3357664 0.2919708 0.2919708 0.2846715 0.3211679
3  0.2773723 0.2700730 0.3722628 0.3065693 0.3284672 0.3138686 0.3138686
4  0.2700730 0.2700730 0.3722628 0.2992701 0.3649635 0.3065693 0.3065693
5  0.2919708 0.3138686 0.3795620 0.3503650 0.3795620 0.3065693 0.2919708
6  0.2773723 0.2919708 0.3941606 0.3430657 0.3649635 0.3284672 0.3138686
7  0.2919708 0.3211679 0.3941606 0.3503650 0.4087591 0.3868613 0.3138686
8  0.2846715 0.2846715 0.3941606 0.3649635 0.3941606 0.3430657 0.3868613
9  0.3211679 0.3138686 0.4160584 0.3649635 0.3430657 0.3430657 0.3795620
10 0.3284672 0.3284672 0.4160584 0.4160584 0.3284672 0.3576642 0.3576642
11 0.3357664 0.2919708 0.4233577 0.3941606 0.3430657 0.4233577 0.3722628
12 0.3795620 0.2846715 0.4233577 0.4233577 0.3357664 0.3722628 0.3722628
13 0.3795620 0.3138686 0.4379562 0.4087591 0.3722628 0.3649635 0.4087591
14 0.3795620 0.2919708 0.4598540 0.4160584 0.3430657 0.4087591 0.4233577
15 0.3284672 0.3065693 0.4598540 0.4452555 0.3649635 0.3649635 0.4306569
   permut.43 permut.44 permut.45 permut.46 permut.47 permut.48 permut.49
1  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.3065693 0.2919708
2  0.3138686 0.2992701 0.3065693 0.2992701 0.3284672 0.2919708 0.3065693
3  0.3284672 0.3138686 0.3357664 0.3065693 0.3430657 0.3065693 0.3211679
4  0.3430657 0.3576642 0.3503650 0.3357664 0.3430657 0.3138686 0.3430657
5  0.3503650 0.3795620 0.3868613 0.3868613 0.3284672 0.3430657 0.3576642
6  0.3722628 0.4160584 0.3649635 0.3868613 0.3357664 0.3576642 0.3284672
7  0.4014599 0.4233577 0.3941606 0.3941606 0.2992701 0.3357664 0.3576642
8  0.3868613 0.4087591 0.3868613 0.4598540 0.3211679 0.3284672 0.3503650
9  0.4087591 0.4306569 0.3868613 0.5401460 0.3430657 0.3649635 0.3649635
10 0.3649635 0.4525547 0.3503650 0.4890511 0.3649635 0.3941606 0.3503650
11 0.4014599 0.4379562 0.3649635 0.5255474 0.3868613 0.3795620 0.3795620
12 0.4306569 0.4452555 0.3430657 0.4598540 0.3795620 0.3795620 0.3576642
13 0.4598540 0.4525547 0.3649635 0.4452555 0.3649635 0.3941606 0.3795620
14 0.4160584 0.4525547 0.3065693 0.4160584 0.3649635 0.3795620 0.3868613
15 0.3722628 0.4452555 0.3211679 0.3795620 0.3284672 0.3576642 0.3357664
   permut.50 permut.51 permut.52 permut.53 permut.54 permut.55 permut.56
1  0.3065693 0.2992701 0.2992701 0.2992701 0.3065693 0.2992701 0.3138686
2  0.2992701 0.3211679 0.2992701 0.3065693 0.3138686 0.3065693 0.3211679
3  0.3211679 0.3430657 0.3138686 0.3138686 0.3138686 0.3138686 0.3357664
4  0.3722628 0.3576642 0.3138686 0.3503650 0.3576642 0.3430657 0.3430657
5  0.3722628 0.3722628 0.3357664 0.3795620 0.3795620 0.3503650 0.3576642
6  0.3430657 0.3649635 0.3430657 0.3868613 0.3868613 0.3649635 0.3503650
7  0.3503650 0.3722628 0.4087591 0.4014599 0.3795620 0.3430657 0.3576642
8  0.3357664 0.3941606 0.4014599 0.4014599 0.3795620 0.3211679 0.3941606
9  0.3649635 0.3941606 0.4087591 0.3649635 0.3941606 0.3284672 0.4671533
10 0.3576642 0.4160584 0.4087591 0.3576642 0.4014599 0.3284672 0.4890511
11 0.3795620 0.4160584 0.3868613 0.3211679 0.4160584 0.3065693 0.4233577
12 0.3722628 0.4160584 0.4014599 0.3503650 0.3576642 0.2919708 0.4525547
13 0.3795620 0.4160584 0.4379562 0.3138686 0.3649635 0.2773723 0.4379562
14 0.3722628 0.4306569 0.4160584 0.3211679 0.3503650 0.2846715 0.4379562
15 0.4014599 0.3503650 0.4525547 0.2992701 0.3868613 0.2846715 0.4160584
   permut.57 permut.58 permut.59 permut.60 permut.61 permut.62 permut.63
1  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
2  0.2919708 0.2992701 0.3138686 0.2992701 0.3357664 0.2992701 0.2992701
3  0.3211679 0.2992701 0.3430657 0.3211679 0.3503650 0.2992701 0.2846715
4  0.3430657 0.3138686 0.3503650 0.3649635 0.3868613 0.3941606 0.2846715
5  0.3430657 0.3284672 0.3576642 0.3722628 0.4160584 0.3503650 0.2846715
6  0.3430657 0.3357664 0.4087591 0.3795620 0.3795620 0.3868613 0.2919708
7  0.3065693 0.3576642 0.4452555 0.3357664 0.3868613 0.3795620 0.3211679
8  0.3357664 0.3722628 0.4671533 0.3576642 0.3868613 0.3576642 0.3868613
9  0.3211679 0.4014599 0.4671533 0.3576642 0.4087591 0.3795620 0.4160584
10 0.3430657 0.4014599 0.4744526 0.3430657 0.3795620 0.3795620 0.3941606
11 0.3722628 0.3868613 0.4671533 0.3868613 0.4014599 0.3941606 0.3795620
12 0.3576642 0.4160584 0.4306569 0.3868613 0.4233577 0.4452555 0.4160584
13 0.3211679 0.4087591 0.4671533 0.3722628 0.4452555 0.4379562 0.3941606
14 0.3503650 0.4087591 0.4525547 0.3722628 0.4671533 0.4379562 0.3722628
15 0.3357664 0.4379562 0.4087591 0.3868613 0.4525547 0.4306569 0.3795620
   permut.64 permut.65 permut.66 permut.67 permut.68 permut.69 permut.70
1  0.2992701 0.2992701 0.2773723 0.2992701 0.2992701 0.2992701 0.2992701
2  0.2992701 0.2992701 0.2481752 0.3065693 0.2992701 0.2700730 0.2992701
3  0.3503650 0.3065693 0.2554745 0.3284672 0.3211679 0.2992701 0.2992701
4  0.3722628 0.2919708 0.2554745 0.3576642 0.3576642 0.3065693 0.3211679
5  0.4233577 0.3211679 0.2554745 0.3941606 0.3941606 0.2992701 0.3211679
6  0.4452555 0.3211679 0.2846715 0.3649635 0.4160584 0.3065693 0.3284672
7  0.4525547 0.2992701 0.2554745 0.3722628 0.3722628 0.3430657 0.3430657
8  0.4379562 0.2992701 0.2846715 0.4014599 0.3795620 0.3430657 0.3503650
9  0.4233577 0.2992701 0.2773723 0.4087591 0.3868613 0.3649635 0.3503650
10 0.4160584 0.3065693 0.3211679 0.4233577 0.4452555 0.3722628 0.3576642
11 0.4306569 0.3211679 0.3138686 0.4014599 0.4598540 0.4014599 0.3649635
12 0.4160584 0.2919708 0.3211679 0.4160584 0.4087591 0.4014599 0.3649635
13 0.4598540 0.2846715 0.3065693 0.4160584 0.3795620 0.3795620 0.3576642
14 0.5036496 0.2627737 0.2919708 0.3941606 0.4087591 0.3576642 0.3649635
15 0.4671533 0.2554745 0.3138686 0.3941606 0.4233577 0.3503650 0.3211679
   permut.71 permut.72 permut.73 permut.74 permut.75 permut.76 permut.77
1  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.3138686 0.2992701
2  0.3138686 0.2773723 0.3138686 0.3284672 0.2992701 0.3503650 0.3065693
3  0.3211679 0.2700730 0.3065693 0.3576642 0.3357664 0.3430657 0.3211679
4  0.3284672 0.2846715 0.3503650 0.3722628 0.3576642 0.3430657 0.3503650
5  0.3284672 0.2627737 0.3941606 0.3795620 0.3503650 0.3722628 0.3795620
6  0.3722628 0.3065693 0.4087591 0.4087591 0.3649635 0.3503650 0.4087591
7  0.3941606 0.3503650 0.3868613 0.4233577 0.4014599 0.3430657 0.3868613
8  0.4014599 0.3649635 0.4379562 0.4671533 0.3722628 0.3211679 0.4452555
9  0.4452555 0.3868613 0.4087591 0.4817518 0.4087591 0.3211679 0.4014599
10 0.4890511 0.4087591 0.3941606 0.4598540 0.4306569 0.3284672 0.4160584
11 0.4890511 0.4014599 0.4014599 0.4890511 0.4306569 0.3503650 0.4233577
12 0.4890511 0.4014599 0.3503650 0.4598540 0.4452555 0.3649635 0.4014599
13 0.4890511 0.4233577 0.3795620 0.4744526 0.4306569 0.3868613 0.4160584
14 0.5109489 0.4014599 0.3503650 0.4525547 0.4452555 0.4379562 0.4087591
15 0.4744526 0.4233577 0.3284672 0.4379562 0.4306569 0.4160584 0.3941606
   permut.78 permut.79 permut.80 permut.81 permut.82 permut.83 permut.84
1  0.3065693 0.2992701 0.2992701 0.2773723 0.2992701 0.2992701 0.3065693
2  0.3211679 0.3284672 0.3138686 0.2846715 0.2992701 0.3065693 0.3211679
3  0.3430657 0.3503650 0.3430657 0.3065693 0.3065693 0.3211679 0.3138686
4  0.3357664 0.3357664 0.3576642 0.3065693 0.2919708 0.3284672 0.3576642
5  0.3722628 0.3649635 0.3576642 0.3138686 0.3649635 0.3722628 0.3357664
6  0.3284672 0.3649635 0.4087591 0.3138686 0.3357664 0.4087591 0.2992701
7  0.3576642 0.3503650 0.4014599 0.2846715 0.3649635 0.4233577 0.3430657
8  0.3576642 0.3576642 0.3941606 0.3138686 0.3576642 0.4160584 0.3576642
9  0.3576642 0.3722628 0.3576642 0.3138686 0.3649635 0.4817518 0.3065693
10 0.3868613 0.3941606 0.4160584 0.3138686 0.4014599 0.4671533 0.3284672
11 0.4087591 0.4160584 0.4087591 0.3138686 0.3868613 0.4817518 0.3357664
12 0.3941606 0.4014599 0.4087591 0.2700730 0.3722628 0.4525547 0.3722628
13 0.4160584 0.4379562 0.4014599 0.2627737 0.3722628 0.4452555 0.3795620
14 0.3795620 0.4306569 0.4160584 0.2846715 0.3649635 0.4379562 0.4087591
15 0.3941606 0.4160584 0.4452555 0.2919708 0.3065693 0.4014599 0.3722628
   permut.85 permut.86 permut.87 permut.88 permut.89 permut.90 permut.91
1  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2919708 0.2992701
2  0.2992701 0.3284672 0.2773723 0.3138686 0.3138686 0.2700730 0.2992701
3  0.3065693 0.3357664 0.2408759 0.3138686 0.3211679 0.2846715 0.3284672
4  0.3211679 0.3211679 0.2992701 0.3284672 0.3211679 0.2919708 0.3284672
5  0.3357664 0.3649635 0.2846715 0.3795620 0.3284672 0.3357664 0.3503650
6  0.3722628 0.3722628 0.3357664 0.4306569 0.4014599 0.3138686 0.3649635
7  0.3795620 0.3722628 0.3430657 0.4452555 0.4233577 0.3430657 0.3941606
8  0.4233577 0.3722628 0.3503650 0.4160584 0.3941606 0.3503650 0.4087591
9  0.4014599 0.4160584 0.3722628 0.4014599 0.3941606 0.3357664 0.4233577
10 0.4014599 0.3503650 0.4014599 0.4233577 0.4306569 0.3722628 0.4452555
11 0.4306569 0.3722628 0.3868613 0.4233577 0.4306569 0.4014599 0.4379562
12 0.4598540 0.3868613 0.4087591 0.3941606 0.4014599 0.3503650 0.4306569
13 0.4233577 0.3649635 0.4087591 0.3941606 0.4160584 0.3649635 0.4306569
14 0.4452555 0.4087591 0.4233577 0.4233577 0.3868613 0.3722628 0.4671533
15 0.4744526 0.4160584 0.3795620 0.4014599 0.3722628 0.3649635 0.4306569
   permut.92 permut.93 permut.94 permut.95 permut.96 permut.97 permut.98
1  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
2  0.3357664 0.3138686 0.3138686 0.3138686 0.3211679 0.2992701 0.2846715
3  0.3430657 0.3430657 0.3065693 0.3211679 0.3065693 0.2700730 0.2773723
4  0.3211679 0.3722628 0.2627737 0.3284672 0.3284672 0.2846715 0.2992701
5  0.3357664 0.4452555 0.2773723 0.3284672 0.3065693 0.2992701 0.2992701
6  0.3503650 0.4525547 0.3065693 0.3722628 0.3430657 0.2919708 0.3138686
7  0.3430657 0.4890511 0.3211679 0.3649635 0.3868613 0.2992701 0.3138686
8  0.3649635 0.4817518 0.3503650 0.3795620 0.3722628 0.2992701 0.3430657
9  0.3284672 0.4598540 0.3430657 0.4233577 0.3795620 0.2700730 0.3722628
10 0.3649635 0.4306569 0.3065693 0.3795620 0.3795620 0.3065693 0.3503650
11 0.3722628 0.4598540 0.3284672 0.4233577 0.3503650 0.3138686 0.4160584
12 0.3868613 0.4452555 0.3649635 0.4306569 0.3649635 0.3284672 0.4087591
13 0.3795620 0.4087591 0.3576642 0.4087591 0.3503650 0.3503650 0.4452555
14 0.4014599 0.4233577 0.3795620 0.4233577 0.3722628 0.3795620 0.4671533
15 0.4306569 0.4452555 0.3722628 0.4233577 0.3576642 0.3649635 0.4744526
   permut.99 permut.100  err.mean      err.sd    err.sterr
1  0.2992701  0.2992701 0.2994161 0.006721993 0.0006721993
2  0.3357664  0.2992701 0.3062044 0.017860665 0.0017860665
3  0.4014599  0.2773723 0.3187591 0.026041504 0.0026041504
4  0.4014599  0.2846715 0.3311679 0.031564681 0.0031564681
5  0.3941606  0.3211679 0.3471533 0.035141405 0.0035141405
6  0.3868613  0.3065693 0.3597810 0.038236126 0.0038236126
7  0.4014599  0.3284672 0.3702190 0.042041092 0.0042041092
8  0.3722628  0.4014599 0.3813869 0.044700223 0.0044700223
9  0.3722628  0.4160584 0.3872993 0.047879354 0.0047879354
10 0.3503650  0.4087591 0.3956204 0.047236367 0.0047236367
11 0.3649635  0.4379562 0.3991971 0.047731598 0.0047731598
12 0.3649635  0.4890511 0.3945985 0.046115882 0.0046115882
13 0.3649635  0.4817518 0.3970073 0.047857712 0.0047857712
14 0.3795620  0.4890511 0.3956204 0.049080262 0.0049080262
15 0.3941606  0.4379562 0.3912409 0.047971211 0.0047971211

$permut.stepwise.qda$best.p
[1] 3

$permut.stepwise.qda$best.error
[1] 0.2773723

$permut.stepwise.qda$best.pda
$permut.stepwise.qda$best.pda$class
  [1] CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
 [19] CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
 [37] CTL PHO PHO PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL
 [55] CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
 [73] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
 [91] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL PHO
[109] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL
[127] PHO CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL
Levels: CTL PHO

$permut.stepwise.qda$best.pda$posterior
                 CTL          PHO
YAL002W   0.66680447 3.331955e-01
YAL038W   0.84577218 1.542278e-01
YAR064W   0.74164147 2.583585e-01
YAR070C   0.79258932 2.074107e-01
YAR071W   0.88546973 1.145303e-01
YBL005W   0.48368769 5.163123e-01
YBL030C   0.60724866 3.927513e-01
YBR006W   0.57725831 4.227417e-01
YBR018C   0.63192026 3.680797e-01
YBR020W   0.60453952 3.954605e-01
YBR093C   0.86128579 1.387142e-01
YBR115C   0.64019174 3.598083e-01
YBR184W   0.67283151 3.271685e-01
YBR213W   0.69841430 3.015857e-01
YBR296C   0.75357584 2.464242e-01
YCL018W   0.57825903 4.217410e-01
YCR037C   0.79900747 2.009925e-01
YCR098C   0.68723891 3.127611e-01
YDL131W   0.55947562 4.405244e-01
YDL182W   0.65994073 3.400593e-01
YDL205C   0.39784820 6.021518e-01
YDL210W   0.72246490 2.775351e-01
YDR011W   0.65613310 3.438669e-01
YDR041W   0.94411073 5.588927e-02
YDR044W   0.57807204 4.219280e-01
YDR054C   0.93547742 6.452258e-02
YDR055W   0.93858161 6.141839e-02
YDR169C   0.97583015 2.416985e-02
YDR234W   0.64765469 3.523453e-01
YDR281C   0.75951298 2.404870e-01
YDR285W   0.59068690 4.093131e-01
YDR303C   0.71488554 2.851145e-01
YDR310C   0.99932769 6.723068e-04
YDR311W   0.99932769 6.723068e-04
YDR406W   0.65159209 3.484079e-01
YDR481C   0.88043692 1.195631e-01
YDR502C   0.64625259 3.537474e-01
YEL017C-A 0.41721895 5.827810e-01
YEL017W   0.41721895 5.827810e-01
YEL021W   0.47983942 5.201606e-01
YEL039C   0.46198996 5.380100e-01
YEL045C   0.68393648 3.160635e-01
YER017C   0.81535141 1.846486e-01
YER019W   0.81535141 1.846486e-01
YER026C   0.57616340 4.238366e-01
YER073W   0.69111430 3.088857e-01
YER086W   0.64738657 3.526134e-01
YER091C   0.78014918 2.198508e-01
YER179W   0.59203642 4.079636e-01
YFL004W   0.93800004 6.199996e-02
YFR030W   0.80279968 1.972003e-01
YGL009C   0.35968370 6.403163e-01
YGL073W   0.71755791 2.824421e-01
YGL213C   0.86351583 1.364842e-01
YGR019W   0.70863641 2.913636e-01
YGR044C   0.28201768 7.179823e-01
YGR088W   0.67152568 3.284743e-01
YGR121C   0.61125355 3.887464e-01
YGR157W   0.82045400 1.795460e-01
YGR233C   0.95969360 4.030640e-02
YGR281W   0.70028150 2.997185e-01
YHL022C   0.55251906 4.474809e-01
YHL036W   0.72270217 2.772978e-01
YHR007C   0.69335571 3.066443e-01
YHR008C   0.61049329 3.895067e-01
YHR014W   0.59137153 4.086285e-01
YHR037W   0.80715276 1.928472e-01
YHR136C   0.89566275 1.043372e-01
YHR137W   0.79931832 2.006817e-01
YHR153C   0.71735455 2.826454e-01
YHR168W   0.99991884 8.115539e-05
YHR215W   0.79258932 2.074107e-01
YIL015W   0.65799478 3.420052e-01
YIL046W   0.54499926 4.550007e-01
YIL072W   0.60962775 3.903723e-01
YIR017C   0.70905529 2.909447e-01
YIR034C   0.63437266 3.656273e-01
YJL012C   0.98944798 1.055202e-02
YJL106W   0.51914512 4.808549e-01
YJL117W   0.82357903 1.764210e-01
YJL153C   0.56166598 4.383340e-01
YJL209W   0.86249740 1.375026e-01
YJL211C   0.79028898 2.097110e-01
YJL219W   0.67860226 3.213977e-01
YJR010W   0.63357071 3.664293e-01
YJR048W   0.64114103 3.588590e-01
YJR073C   0.74706579 2.529342e-01
YJR094C   0.63795951 3.620405e-01
YJR137C   0.83283851 1.671615e-01
YJR152W   0.61134632 3.886537e-01
YKL001C   0.62741077 3.725892e-01
YKL182W   0.53919275 4.608073e-01
YKL216W   0.62784204 3.721580e-01
YKR039W   0.61671358 3.832864e-01
YKR048C   0.76756556 2.324344e-01
YKR050W   0.84720978 1.527902e-01
YKR069W   0.82876272 1.712373e-01
YLR081W   0.66883989 3.311601e-01
YLR142W   0.67436679 3.256332e-01
YLR180W   0.65071001 3.492900e-01
YLR263W   0.28736887 7.126311e-01
YLR303W   0.86355975 1.364402e-01
YLR329W   0.68819293 3.118071e-01
YLR420W   0.61281321 3.871868e-01
YLR438W   0.74764790 2.523521e-01
YML051W   0.71574800 2.842520e-01
YML054C   0.55442564 4.455744e-01
YML075C   0.41598554 5.840145e-01
YML121W   0.87942804 1.205720e-01
YML123C   0.80342510 1.965749e-01
YMR108W   0.60125945 3.987406e-01
YMR133W   0.56374488 4.362551e-01
YNL052W   0.79553629 2.044637e-01
YNL061W   0.89432361 1.056764e-01
YNL063W   0.74645465 2.535453e-01
YNL064C   0.74645465 2.535453e-01
YNL104C   0.77435881 2.256412e-01
YNL142W   0.70685314 2.931469e-01
YNL210W   0.61614167 3.838583e-01
YNL241C   0.66907462 3.309254e-01
YNL277W   0.71191901 2.880810e-01
YNR001C   0.09941869 9.005813e-01
YNR050C   0.73316658 2.668334e-01
YOL006C   0.59423840 4.057616e-01
YOR065W   0.71537715 2.846229e-01
YOR120W   0.54279936 4.572006e-01
YOR153W   0.34616540 6.538346e-01
YOR328W   0.65915311 3.408469e-01
YOR351C   0.64766982 3.523302e-01
YOR375C   0.28210008 7.178999e-01
YPL068C   0.88124182 1.187582e-01
YPL111W   0.62334105 3.766589e-01
YPL231W   0.69104694 3.089531e-01
YPR065W   0.60298393 3.970161e-01
YPR138C   0.74380712 2.561929e-01
YPR145W   0.63146955 3.685305e-01
YPR167C   0.75071440 2.492856e-01

$permut.stepwise.qda$best.pda$call
qda(x = data.training, grouping = labels.training, CV = loo, 
    na.action = na.omit)

$permut.stepwise.qda$best.pda$training.label
  [1] CTL CTL CTL CTL PHO CTL PHO PHO CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL
 [19] CTL PHO PHO PHO CTL CTL CTL PHO CTL CTL PHO CTL CTL CTL CTL CTL PHO CTL
 [37] CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL PHO CTL PHO CTL PHO PHO PHO CTL
 [55] CTL PHO CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL PHO CTL PHO PHO CTL
 [73] CTL CTL CTL CTL PHO CTL CTL CTL CTL PHO CTL CTL CTL PHO CTL CTL CTL CTL
 [91] CTL CTL PHO PHO CTL PHO CTL CTL CTL PHO PHO PHO CTL PHO CTL CTL CTL CTL
[109] PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO PHO PHO PHO CTL CTL CTL
[127] PHO CTL PHO PHO CTL CTL CTL CTL PHO CTL PHO
Levels: CTL PHO

$permut.stepwise.qda$best.pda$pda.method
[1] "qda"

$permut.stepwise.qda$best.pda$loo
[1] TRUE

$permut.stepwise.qda$best.pda$validation
[1] "LOO"

$permut.stepwise.qda$best.pda$confusion
      true
object CTL PHO
   CTL  91  33
   PHO   5   8
attr(,"error")
[1] 0.2773723



$permut.pc.stepwise.qda
$permut.pc.stepwise.qda$confusion.table
        error CTL.CTL CTL.PHO PHO.CTL PHO.PHO
1   0.2992701      85      11      30      11
2   0.2992701      96       0      41       0
3   0.2992701      96       0      41       0
4   0.2992701      96       0      41       0
5   0.2992701      96       0      41       0
6   0.2992701      96       0      41       0
7   0.3211679      93       3      41       0
8   0.2700730      92       4      33       8
9   0.2919708      89       7      33       8
10  0.2992701      96       0      41       0
11  0.2992701      96       0      41       0
12  0.2919708      90       6      34       7
13  0.2992701      90       6      35       6
14  0.2992701      96       0      41       0
15  0.3065693      91       5      37       4
16  0.2700730      94       2      35       6
17  0.2992701      96       0      41       0
18  0.2992701      96       0      41       0
19  0.2992701      96       0      41       0
20  0.2992701      96       0      41       0
21  0.2992701      96       0      41       0
22  0.2773723      87       9      29      12
23  0.2846715      89       7      32       9
24  0.2992701      87       9      32       9
25  0.2992701      96       0      41       0
26  0.2992701      96       0      41       0
27  0.2992701      96       0      41       0
28  0.2992701      96       0      41       0
29  0.2992701      96       0      41       0
30  0.2992701      96       0      41       0
31  0.2992701      96       0      41       0
32  0.2992701      96       0      41       0
33  0.2992701      88       8      33       8
34  0.2992701      96       0      41       0
35  0.2992701      96       0      41       0
36  0.2992701      89       7      34       7
37  0.2992701      96       0      41       0
38  0.2919708      89       7      33       8
39  0.2992701      96       0      41       0
40  0.2992701      96       0      41       0
41  0.3065693      90       6      36       5
42  0.2992701      84      12      29      12
43  0.2992701      96       0      41       0
44  0.3065693      87       9      33       8
45  0.2992701      83      13      28      13
46  0.2992701      96       0      41       0
47  0.2992701      96       0      41       0
48  0.2992701      96       0      41       0
49  0.2627737      92       4      32       9
50  0.2992701      96       0      41       0
51  0.2700730      90       6      31      10
52  0.2992701      84      12      29      12
53  0.2992701      96       0      41       0
54  0.2919708      91       5      35       6
55  0.2481752      92       4      30      11
56  0.2992701      96       0      41       0
57  0.2773723      87       9      29      12
58  0.2992701      96       0      41       0
59  0.2992701      96       0      41       0
60  0.2992701      96       0      41       0
61  0.2627737      92       4      32       9
62  0.2992701      96       0      41       0
63  0.2992701      86      10      31      10
64  0.2846715      92       4      35       6
65  0.2992701      90       6      35       6
66  0.2992701      96       0      41       0
67  0.2919708      94       2      38       3
68  0.2992701      96       0      41       0
69  0.2992701      96       0      41       0
70  0.2554745      92       4      31      10
71  0.2992701      96       0      41       0
72  0.2773723      93       3      35       6
73  0.2992701      96       0      41       0
74  0.2992701      96       0      41       0
75  0.3065693      93       3      39       2
76  0.3211679      93       3      41       0
77  0.2846715      91       5      34       7
78  0.2773723      81      15      23      18
79  0.3138686      91       5      38       3
80  0.2992701      96       0      41       0
81  0.2627737      90       6      30      11
82  0.3065693      92       4      38       3
83  0.3065693      93       3      39       2
84  0.2992701      94       2      39       2
85  0.2992701      96       0      41       0
86  0.2992701      96       0      41       0
87  0.2992701      96       0      41       0
88  0.3138686      91       5      38       3
89  0.2992701      96       0      41       0
90  0.2992701      96       0      41       0
91  0.2992701      91       5      36       5
92  0.2992701      96       0      41       0
93  0.2992701      96       0      41       0
94  0.2919708      90       6      34       7
95  0.2627737      92       4      32       9
96  0.2992701      96       0      41       0
97  0.2992701      96       0      41       0
98  0.2992701      91       5      36       5
99  0.2846715      90       6      33       8
100 0.2846715      90       6      33       8

$permut.pc.stepwise.qda$errors
    permut.1  permut.2  permut.3  permut.4  permut.5  permut.6  permut.7
1  0.3138686 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.3211679
2  0.3284672 0.3357664 0.3211679 0.3284672 0.2992701 0.2992701 0.3284672
3  0.3430657 0.3430657 0.3503650 0.3138686 0.2992701 0.3211679 0.3357664
4  0.3065693 0.3649635 0.3357664 0.3138686 0.3211679 0.3868613 0.3284672
5  0.2992701 0.3576642 0.3576642 0.3211679 0.3284672 0.3576642 0.3503650
6  0.3211679 0.3576642 0.3868613 0.3576642 0.3649635 0.4160584 0.3357664
7  0.2992701 0.3795620 0.4014599 0.3722628 0.3649635 0.3868613 0.3503650
8  0.3138686 0.3941606 0.4087591 0.4014599 0.3722628 0.4087591 0.4014599
9  0.3357664 0.3941606 0.3941606 0.4306569 0.3868613 0.4087591 0.3795620
10 0.3576642 0.3868613 0.3795620 0.4233577 0.4014599 0.4014599 0.4160584
11 0.3576642 0.3722628 0.3868613 0.4379562 0.4160584 0.4087591 0.4087591
12 0.3503650 0.3649635 0.3795620 0.4744526 0.4087591 0.4233577 0.3868613
13 0.3503650 0.3868613 0.4379562 0.4306569 0.4379562 0.4160584 0.3868613
14 0.3868613 0.3868613 0.4525547 0.4598540 0.4087591 0.3795620 0.3795620
15 0.3576642 0.3795620 0.4525547 0.4598540 0.4160584 0.3284672 0.3503650
    permut.8  permut.9 permut.10 permut.11 permut.12 permut.13 permut.14
1  0.2846715 0.2992701 0.2992701 0.2992701 0.2919708 0.3138686 0.2992701
2  0.2700730 0.3065693 0.2992701 0.2992701 0.2919708 0.3284672 0.2992701
3  0.2773723 0.3211679 0.3138686 0.3065693 0.2992701 0.2992701 0.3138686
4  0.3138686 0.2919708 0.3211679 0.3284672 0.3211679 0.3065693 0.3138686
5  0.3138686 0.3357664 0.3649635 0.3430657 0.3503650 0.3065693 0.3430657
6  0.3284672 0.3138686 0.3649635 0.3284672 0.3649635 0.3211679 0.3649635
7  0.3576642 0.3430657 0.4160584 0.3722628 0.3941606 0.3576642 0.3941606
8  0.3722628 0.3430657 0.4525547 0.4014599 0.4160584 0.3722628 0.4160584
9  0.3430657 0.3357664 0.4160584 0.3941606 0.4233577 0.3868613 0.4744526
10 0.3430657 0.3357664 0.4598540 0.4160584 0.4160584 0.3868613 0.4306569
11 0.3576642 0.3722628 0.4890511 0.4598540 0.4306569 0.3941606 0.4525547
12 0.3722628 0.3941606 0.4671533 0.4014599 0.4233577 0.3795620 0.4817518
13 0.4014599 0.3868613 0.4671533 0.4087591 0.3941606 0.3430657 0.4744526
14 0.4379562 0.3941606 0.4525547 0.4014599 0.4160584 0.3357664 0.4452555
15 0.4233577 0.3868613 0.4452555 0.4306569 0.4087591 0.3211679 0.4744526
   permut.15 permut.16 permut.17 permut.18 permut.19 permut.20 permut.21
1  0.3065693 0.2700730 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
2  0.3065693 0.2700730 0.3138686 0.2992701 0.3138686 0.3065693 0.3138686
3  0.3065693 0.3138686 0.3138686 0.2992701 0.3065693 0.3065693 0.3211679
4  0.3211679 0.2846715 0.3284672 0.3138686 0.3138686 0.3941606 0.3503650
5  0.3430657 0.3138686 0.3138686 0.3430657 0.3211679 0.3868613 0.3722628
6  0.3138686 0.3065693 0.3065693 0.3503650 0.3138686 0.4452555 0.3649635
7  0.3211679 0.3430657 0.3211679 0.3722628 0.3138686 0.4817518 0.3941606
8  0.3284672 0.3284672 0.3211679 0.3722628 0.3357664 0.4963504 0.3795620
9  0.3284672 0.3503650 0.3503650 0.3941606 0.3430657 0.4379562 0.4160584
10 0.3430657 0.3576642 0.3576642 0.4306569 0.3357664 0.4306569 0.4014599
11 0.3868613 0.3430657 0.3795620 0.3941606 0.3503650 0.4598540 0.3941606
12 0.3868613 0.3503650 0.4233577 0.4087591 0.3649635 0.3868613 0.3868613
13 0.3284672 0.3430657 0.4014599 0.3868613 0.3503650 0.3868613 0.4014599
14 0.3576642 0.3576642 0.4014599 0.4014599 0.3430657 0.3795620 0.4087591
15 0.3941606 0.3868613 0.4014599 0.3868613 0.3503650 0.3722628 0.4379562
   permut.22 permut.23 permut.24 permut.25 permut.26 permut.27 permut.28
1  0.3138686 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
2  0.2919708 0.3138686 0.3065693 0.3065693 0.3138686 0.3065693 0.3065693
3  0.2846715 0.2846715 0.3138686 0.3138686 0.3576642 0.3211679 0.3065693
4  0.2919708 0.2919708 0.3284672 0.3065693 0.3795620 0.3211679 0.3357664
5  0.2773723 0.2992701 0.3284672 0.3430657 0.3649635 0.3503650 0.3503650
6  0.3211679 0.2992701 0.2992701 0.3941606 0.4014599 0.3357664 0.3430657
7  0.3211679 0.3284672 0.3138686 0.3722628 0.4087591 0.3430657 0.3941606
8  0.3722628 0.3430657 0.3357664 0.3576642 0.3795620 0.3576642 0.3576642
9  0.3357664 0.3503650 0.3795620 0.3722628 0.4452555 0.3868613 0.3868613
10 0.3503650 0.3357664 0.3941606 0.3430657 0.4379562 0.4306569 0.3430657
11 0.3430657 0.3503650 0.4671533 0.3284672 0.4306569 0.4087591 0.3868613
12 0.3722628 0.3430657 0.4379562 0.3576642 0.4233577 0.4379562 0.3941606
13 0.3503650 0.3722628 0.4087591 0.3284672 0.4379562 0.3941606 0.4014599
14 0.3576642 0.4014599 0.4306569 0.3795620 0.4306569 0.4160584 0.4014599
15 0.3722628 0.3941606 0.4306569 0.3357664 0.4087591 0.4160584 0.3868613
   permut.29 permut.30 permut.31 permut.32 permut.33 permut.34 permut.35
1  0.2992701 0.2992701 0.2992701 0.2992701 0.3065693 0.2992701 0.2992701
2  0.3065693 0.2992701 0.3211679 0.3065693 0.3357664 0.3065693 0.3430657
3  0.3284672 0.3211679 0.3430657 0.3138686 0.2992701 0.3138686 0.3649635
4  0.3576642 0.3065693 0.3576642 0.3065693 0.3065693 0.3503650 0.3503650
5  0.3649635 0.3284672 0.3722628 0.3357664 0.3065693 0.3576642 0.3430657
6  0.3795620 0.3503650 0.3722628 0.3065693 0.3138686 0.3503650 0.3576642
7  0.3941606 0.3941606 0.3722628 0.3430657 0.3503650 0.3430657 0.3868613
8  0.4306569 0.3795620 0.3649635 0.3138686 0.3576642 0.3649635 0.4160584
9  0.4233577 0.4087591 0.3795620 0.3211679 0.3357664 0.4014599 0.4160584
10 0.4525547 0.4306569 0.4306569 0.3284672 0.3649635 0.4306569 0.3941606
11 0.4525547 0.4233577 0.3868613 0.3576642 0.3576642 0.4306569 0.3649635
12 0.4890511 0.4233577 0.4160584 0.3503650 0.3649635 0.4379562 0.3868613
13 0.4963504 0.3722628 0.4014599 0.3795620 0.4160584 0.4744526 0.3941606
14 0.4598540 0.3065693 0.4233577 0.3576642 0.4160584 0.4744526 0.4087591
15 0.4598540 0.3795620 0.4379562 0.3576642 0.4379562 0.4671533 0.4379562
   permut.36 permut.37 permut.38 permut.39 permut.40 permut.41 permut.42
1  0.2992701 0.2992701 0.3211679 0.2992701 0.2992701 0.3138686 0.2992701
2  0.3065693 0.3065693 0.3284672 0.3211679 0.2992701 0.3065693 0.3065693
3  0.3138686 0.3357664 0.3211679 0.3284672 0.3357664 0.3138686 0.3284672
4  0.3284672 0.3357664 0.2919708 0.3357664 0.3503650 0.3430657 0.3211679
5  0.3211679 0.3284672 0.3284672 0.3576642 0.3576642 0.3430657 0.3357664
6  0.3065693 0.3430657 0.3211679 0.3868613 0.3576642 0.3430657 0.3211679
7  0.3138686 0.3430657 0.3357664 0.3722628 0.3868613 0.3868613 0.3284672
8  0.3795620 0.3722628 0.3430657 0.4014599 0.4087591 0.3795620 0.3284672
9  0.3576642 0.3722628 0.3284672 0.4379562 0.4525547 0.3868613 0.2992701
10 0.3795620 0.3576642 0.3649635 0.4087591 0.4525547 0.3722628 0.3138686
11 0.3868613 0.3430657 0.3722628 0.4087591 0.4379562 0.3722628 0.3430657
12 0.3576642 0.3649635 0.4160584 0.4087591 0.4379562 0.3941606 0.3284672
13 0.3649635 0.3430657 0.3868613 0.4525547 0.4160584 0.3649635 0.3430657
14 0.3722628 0.3795620 0.3503650 0.4379562 0.4306569 0.4014599 0.3357664
15 0.3795620 0.3795620 0.3722628 0.4233577 0.4379562 0.3795620 0.3576642
   permut.43 permut.44 permut.45 permut.46 permut.47 permut.48 permut.49
1  0.2992701 0.3065693 0.2992701 0.2992701 0.2992701 0.2992701 0.2919708
2  0.3138686 0.3284672 0.3138686 0.2992701 0.2992701 0.2992701 0.2627737
3  0.3211679 0.3576642 0.3065693 0.3065693 0.3138686 0.3284672 0.2846715
4  0.3722628 0.3357664 0.3138686 0.3722628 0.3284672 0.3430657 0.2992701
5  0.3576642 0.3430657 0.3430657 0.3722628 0.3430657 0.3722628 0.3211679
6  0.3795620 0.3065693 0.3430657 0.4014599 0.3503650 0.4379562 0.3722628
7  0.3941606 0.3503650 0.3138686 0.3941606 0.3503650 0.4598540 0.3649635
8  0.3430657 0.3357664 0.3284672 0.3868613 0.3722628 0.4306569 0.4160584
9  0.3430657 0.3357664 0.3649635 0.4014599 0.3722628 0.4452555 0.4160584
10 0.3722628 0.3430657 0.4014599 0.4452555 0.3868613 0.4379562 0.4379562
11 0.4087591 0.3868613 0.3430657 0.4087591 0.3868613 0.4525547 0.4525547
12 0.4233577 0.3941606 0.3722628 0.3868613 0.3941606 0.4452555 0.4671533
13 0.4452555 0.3868613 0.3430657 0.4014599 0.3868613 0.3795620 0.4671533
14 0.4160584 0.3868613 0.3357664 0.3941606 0.4233577 0.3649635 0.4160584
15 0.4014599 0.3941606 0.2992701 0.4525547 0.4452555 0.4087591 0.4233577
   permut.50 permut.51 permut.52 permut.53 permut.54 permut.55 permut.56
1  0.2992701 0.2992701 0.3138686 0.2992701 0.2919708 0.2919708 0.2992701
2  0.3065693 0.3357664 0.3138686 0.2992701 0.2919708 0.2627737 0.3065693
3  0.3211679 0.2773723 0.3284672 0.3138686 0.3065693 0.2481752 0.3430657
4  0.3430657 0.2700730 0.3357664 0.3576642 0.3138686 0.2554745 0.3357664
5  0.3503650 0.2846715 0.3503650 0.4087591 0.3138686 0.3065693 0.3576642
6  0.3868613 0.3211679 0.3649635 0.4160584 0.3284672 0.3284672 0.3795620
7  0.4014599 0.3284672 0.3357664 0.4452555 0.3503650 0.3357664 0.4087591
8  0.4233577 0.3576642 0.3795620 0.4014599 0.3722628 0.3430657 0.3722628
9  0.4233577 0.3576642 0.3576642 0.3868613 0.3868613 0.3868613 0.3941606
10 0.4306569 0.3722628 0.3576642 0.4014599 0.3649635 0.3941606 0.3211679
11 0.4379562 0.3503650 0.3722628 0.3941606 0.3649635 0.3868613 0.3868613
12 0.4744526 0.3649635 0.4014599 0.4014599 0.3868613 0.4087591 0.3649635
13 0.4306569 0.3649635 0.3284672 0.4379562 0.4452555 0.4087591 0.3941606
14 0.4160584 0.3503650 0.3284672 0.4306569 0.4014599 0.4160584 0.3941606
15 0.4233577 0.3722628 0.2992701 0.4525547 0.4087591 0.4379562 0.4160584
   permut.57 permut.58 permut.59 permut.60 permut.61 permut.62 permut.63
1  0.2992701 0.2992701 0.2992701 0.2992701 0.3211679 0.2992701 0.2992701
2  0.3138686 0.3065693 0.3065693 0.2992701 0.2627737 0.3211679 0.2992701
3  0.3211679 0.3138686 0.3211679 0.3065693 0.2700730 0.3430657 0.3211679
4  0.3357664 0.3138686 0.3503650 0.3138686 0.2773723 0.3503650 0.3430657
5  0.3211679 0.3211679 0.3430657 0.3284672 0.2919708 0.3576642 0.3211679
6  0.3211679 0.3503650 0.3576642 0.3065693 0.2919708 0.3576642 0.3138686
7  0.2919708 0.3576642 0.3941606 0.3503650 0.3138686 0.3649635 0.2992701
8  0.2773723 0.3868613 0.4233577 0.3795620 0.3138686 0.3503650 0.3284672
9  0.3065693 0.3649635 0.4671533 0.3722628 0.3430657 0.3941606 0.3211679
10 0.3357664 0.3722628 0.4525547 0.3795620 0.3795620 0.4087591 0.3065693
11 0.3795620 0.4014599 0.4598540 0.3795620 0.3576642 0.4014599 0.3722628
12 0.3941606 0.3868613 0.4671533 0.3722628 0.3503650 0.3941606 0.3576642
13 0.3722628 0.3941606 0.4379562 0.4160584 0.3576642 0.3649635 0.3138686
14 0.3941606 0.3941606 0.4452555 0.3795620 0.3430657 0.3795620 0.3211679
15 0.3722628 0.4160584 0.4087591 0.3795620 0.3795620 0.3576642 0.3503650
   permut.64 permut.65 permut.66 permut.67 permut.68 permut.69 permut.70
1  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701
2  0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.2992701 0.3138686
3  0.2992701 0.3138686 0.3138686 0.2992701 0.3284672 0.2992701 0.2554745
4  0.2846715 0.3503650 0.3284672 0.2919708 0.3284672 0.3430657 0.2992701
5  0.3138686 0.3284672 0.3357664 0.3138686 0.3357664 0.3430657 0.3211679
6  0.3357664 0.3211679 0.3576642 0.3503650 0.3357664 0.3576642 0.3576642
7  0.3649635 0.3284672 0.3576642 0.3576642 0.3868613 0.4014599 0.3430657
8  0.3722628 0.3430657 0.3649635 0.4379562 0.3722628 0.4014599 0.3649635
9  0.3941606 0.3357664 0.3795620 0.4160584 0.3868613 0.4379562 0.3795620
10 0.4306569 0.3795620 0.3649635 0.4671533 0.4014599 0.4598540 0.3576642
11 0.4525547 0.3795620 0.3649635 0.4817518 0.4087591 0.4233577 0.3284672
12 0.4671533 0.3868613 0.3649635 0.4817518 0.3649635 0.4452555 0.3284672
13 0.5182482 0.4014599 0.3649635 0.4671533 0.4014599 0.4671533 0.3357664
14 0.4890511 0.4087591 0.3722628 0.4233577 0.3868613 0.4452555 0.3503650
15 0.4744526 0.4525547 0.3722628 0.4160584 0.3649635 0.4379562 0.3576642
   permut.71 permut.72 permut.73 permut.74 permut.75 permut.76 permut.77
1  0.2992701 0.2846715 0.2992701 0.2992701 0.3211679 0.3211679 0.2919708
2  0.3211679 0.2773723 0.3065693 0.3138686 0.3065693 0.3211679 0.2846715
3  0.3138686 0.2846715 0.3211679 0.3284672 0.3430657 0.3211679 0.2919708
4  0.3357664 0.3065693 0.3430657 0.3284672 0.3576642 0.3576642 0.3576642
5  0.3430657 0.3357664 0.3576642 0.3503650 0.3576642 0.3941606 0.3357664
6  0.3576642 0.3211679 0.4087591 0.4014599 0.4014599 0.3722628 0.3576642
7  0.3722628 0.3722628 0.4233577 0.3795620 0.4160584 0.4087591 0.3576642
8  0.3503650 0.3795620 0.4160584 0.3941606 0.3868613 0.4160584 0.3722628
9  0.3138686 0.3722628 0.4306569 0.3868613 0.3795620 0.4160584 0.3941606
10 0.3576642 0.3868613 0.4379562 0.4014599 0.3795620 0.4306569 0.3941606
11 0.3576642 0.3795620 0.4379562 0.4452555 0.4160584 0.4160584 0.4160584
12 0.4014599 0.3795620 0.4598540 0.4087591 0.4306569 0.4233577 0.4233577
13 0.3795620 0.3722628 0.4160584 0.4087591 0.4306569 0.4014599 0.4087591
14 0.3722628 0.3722628 0.3649635 0.4306569 0.4233577 0.4160584 0.3795620
15 0.3649635 0.3795620 0.3649635 0.3941606 0.4379562 0.3941606 0.3941606
   permut.78 permut.79 permut.80 permut.81 permut.82 permut.83 permut.84
1  0.2919708 0.3138686 0.2992701 0.2992701 0.3065693 0.3065693 0.2992701
2  0.2773723 0.3138686 0.3284672 0.2992701 0.3065693 0.3065693 0.3065693
3  0.2846715 0.3357664 0.3357664 0.2992701 0.3284672 0.3138686 0.2992701
4  0.2992701 0.3576642 0.3649635 0.3065693 0.3430657 0.3357664 0.3211679
5  0.2919708 0.3430657 0.3795620 0.3211679 0.3576642 0.3357664 0.3284672
6  0.3138686 0.3722628 0.3576642 0.2627737 0.3722628 0.3503650 0.3868613
7  0.3211679 0.3722628 0.4014599 0.2627737 0.3503650 0.3430657 0.3722628
8  0.2992701 0.3576642 0.3868613 0.2773723 0.3941606 0.3357664 0.3649635
9  0.3284672 0.3722628 0.4452555 0.2846715 0.4306569 0.3357664 0.4160584
10 0.2846715 0.3649635 0.4306569 0.3357664 0.4306569 0.3649635 0.3503650
11 0.2773723 0.3649635 0.4525547 0.3284672 0.4014599 0.3211679 0.3138686
12 0.3065693 0.3941606 0.4379562 0.3284672 0.3941606 0.3430657 0.3503650
13 0.2992701 0.3868613 0.4671533 0.3503650 0.4087591 0.3357664 0.3868613
14 0.2992701 0.3722628 0.3722628 0.3503650 0.4014599 0.3576642 0.3941606
15 0.3138686 0.3941606 0.3795620 0.3284672 0.3941606 0.3503650 0.3649635
   permut.85 permut.86 permut.87 permut.88 permut.89 permut.90 permut.91
1  0.2992701 0.2992701 0.2992701 0.3138686 0.2992701 0.2992701 0.2992701
2  0.3065693 0.3065693 0.3284672 0.3211679 0.3138686 0.3065693 0.2992701
3  0.3211679 0.3211679 0.3065693 0.3503650 0.3357664 0.3211679 0.3211679
4  0.3503650 0.3357664 0.3065693 0.3576642 0.3284672 0.3357664 0.3357664
5  0.3357664 0.3941606 0.3284672 0.3868613 0.3503650 0.3357664 0.3138686
6  0.3722628 0.4306569 0.3284672 0.3941606 0.3868613 0.4087591 0.3357664
7  0.3941606 0.4379562 0.3357664 0.4306569 0.3868613 0.4014599 0.3503650
8  0.4087591 0.5036496 0.3138686 0.3941606 0.3941606 0.4087591 0.3722628
9  0.4233577 0.4744526 0.3357664 0.4379562 0.4160584 0.4087591 0.3941606
10 0.4233577 0.4525547 0.4087591 0.4598540 0.3795620 0.4233577 0.4452555
11 0.4452555 0.4087591 0.4014599 0.4671533 0.4233577 0.4306569 0.4452555
12 0.4963504 0.4598540 0.3576642 0.4525547 0.3941606 0.4306569 0.4233577
13 0.4817518 0.4671533 0.3722628 0.4452555 0.3941606 0.4525547 0.4087591
14 0.4233577 0.4671533 0.3576642 0.4379562 0.3430657 0.4379562 0.4306569
15 0.4452555 0.4817518 0.3868613 0.4452555 0.3576642 0.4452555 0.4452555
   permut.92 permut.93 permut.94 permut.95 permut.96 permut.97 permut.98
1  0.2992701 0.2992701 0.2992701 0.2627737 0.2992701 0.2992701 0.2992701
2  0.3065693 0.3430657 0.2919708 0.2700730 0.3138686 0.3284672 0.3211679
3  0.3211679 0.3138686 0.3065693 0.2700730 0.3284672 0.3357664 0.3138686
4  0.3576642 0.3138686 0.3357664 0.2700730 0.3138686 0.3430657 0.3503650
5  0.3795620 0.3138686 0.3211679 0.2992701 0.3357664 0.3722628 0.3357664
6  0.4014599 0.3138686 0.3430657 0.3284672 0.3357664 0.3868613 0.3430657
7  0.4744526 0.3430657 0.3722628 0.3211679 0.3722628 0.3795620 0.3284672
8  0.4817518 0.3795620 0.3649635 0.3649635 0.3795620 0.3868613 0.3357664
9  0.4452555 0.4014599 0.4160584 0.3795620 0.3795620 0.4525547 0.3649635
10 0.4598540 0.3868613 0.4160584 0.3722628 0.3868613 0.4525547 0.3576642
11 0.4525547 0.3138686 0.4233577 0.4014599 0.4306569 0.4525547 0.3357664
12 0.4379562 0.3284672 0.4525547 0.4379562 0.4087591 0.4671533 0.3649635
13 0.4452555 0.3649635 0.4452555 0.4598540 0.4379562 0.4671533 0.3649635
14 0.4233577 0.3503650 0.4598540 0.4671533 0.4233577 0.4671533 0.3941606
15 0.4233577 0.3503650 0.4744526 0.4744526 0.4452555 0.4817518 0.3868613
   permut.99 permut.100  err.mean      err.sd    err.sterr
1  0.2919708  0.2992701 0.3002920 0.008429748 0.0008429748
2  0.2919708  0.2992701 0.3067153 0.016271468 0.0016271468
3  0.2846715  0.2846715 0.3145255 0.021035262 0.0021035262
4  0.3211679  0.2846715 0.3280292 0.026222016 0.0026222016
5  0.3138686  0.3284672 0.3389781 0.024819687 0.0024819687
6  0.3284672  0.3576642 0.3519708 0.034868666 0.0034868666
7  0.3284672  0.3649635 0.3659124 0.038813905 0.0038813905
8  0.3503650  0.3649635 0.3749635 0.039961639 0.0039961639
9  0.3430657  0.3868613 0.3854015 0.040766224 0.0040766224
10 0.3065693  0.4160584 0.3918978 0.041598595 0.0041598595
11 0.3357664  0.4598540 0.3968613 0.043445911 0.0043445911
12 0.3357664  0.4963504 0.4023358 0.043130440 0.0043130440
13 0.3576642  0.4306569 0.4010219 0.044099562 0.0044099562
14 0.3649635  0.4160584 0.3973723 0.039510157 0.0039510157
15 0.3868613  0.4160584 0.4009489 0.042247644 0.0042247644

$permut.pc.stepwise.qda$best.p
[1] 4

$permut.pc.stepwise.qda$best.error
[1] 0.2846715

$permut.pc.stepwise.qda$best.pda
$permut.pc.stepwise.qda$best.pda$class
  [1] CTL PHO CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
 [19] CTL PHO PHO CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL
 [37] CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL
 [55] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL
 [73] CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
 [91] CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[109] CTL CTL PHO CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[127] CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL
Levels: CTL PHO

$permut.pc.stepwise.qda$best.pda$posterior
                CTL          PHO
YAL002W   0.7491025 0.2508974695
YAL038W   0.4679709 0.5320290530
YAR064W   0.7203232 0.2796767975
YAR070C   0.7259507 0.2740492869
YAR071W   0.5541909 0.4458090689
YBL005W   0.3910303 0.6089696537
YBL030C   0.6209536 0.3790464177
YBR006W   0.6590841 0.3409158869
YBR018C   0.5975374 0.4024626370
YBR020W   0.5395021 0.4604979483
YBR093C   0.7643216 0.2356784199
YBR115C   0.7735615 0.2264384758
YBR184W   0.9477160 0.0522839739
YBR213W   0.9727205 0.0272795357
YBR296C   0.8181459 0.1818540620
YCL018W   0.6971307 0.3028693218
YCR037C   0.7469235 0.2530764815
YCR098C   0.7727679 0.2272321018
YDL131W   0.5065127 0.4934873092
YDL182W   0.3760487 0.6239512570
YDL205C   0.3837809 0.6162191224
YDL210W   0.6054751 0.3945248790
YDR011W   0.6140443 0.3859556504
YDR041W   0.3799035 0.6200964981
YDR044W   0.5679508 0.4320492432
YDR054C   0.6140106 0.3859893847
YDR055W   0.6012198 0.3987802114
YDR169C   0.7395153 0.2604847160
YDR234W   0.7389652 0.2610347696
YDR281C   0.7534304 0.2465695508
YDR285W   0.7818318 0.2181681678
YDR303C   0.8201308 0.1798691560
YDR310C   0.6029355 0.3970644925
YDR311W   0.3573530 0.6426470007
YDR406W   0.6617871 0.3382129175
YDR481C   0.5802802 0.4197197700
YDR502C   0.9877020 0.0122979862
YEL017C-A 0.9388253 0.0611746926
YEL017W   0.7755383 0.2244617059
YEL021W   0.5360527 0.4639472768
YEL039C   0.3973713 0.6026287004
YEL045C   0.8114778 0.1885221541
YER017C   0.6555450 0.3444549790
YER019W   0.6534464 0.3465536277
YER026C   0.8126064 0.1873936137
YER073W   0.8259241 0.1740758704
YER086W   0.5021238 0.4978762169
YER091C   0.9993272 0.0006728442
YER179W   0.7366533 0.2633467097
YFL004W   0.5179253 0.4820746891
YFR030W   0.9822766 0.0177233984
YGL009C   0.8277378 0.1722622352
YGL073W   0.4790595 0.5209404541
YGL213C   0.6956444 0.3043556022
YGR019W   0.7170043 0.2829957394
YGR044C   0.8216997 0.1783003368
YGR088W   0.5740929 0.4259070875
YGR121C   0.5173792 0.4826208254
YGR157W   0.9703811 0.0296188531
YGR233C   0.6826900 0.3173099663
YGR281W   0.8165453 0.1834547050
YHL022C   0.6645431 0.3354569286
YHL036W   0.9976777 0.0023223189
YHR007C   0.6017444 0.3982555825
YHR008C   0.5315684 0.4684315772
YHR014W   0.7029731 0.2970268776
YHR037W   0.6671013 0.3328987172
YHR136C   0.8027607 0.1972392585
YHR137W   0.9995351 0.0004649391
YHR153C   0.7111181 0.2888818544
YHR168W   0.3100868 0.6899132489
YHR215W   0.5541909 0.4458090689
YIL015W   0.6877919 0.3122081228
YIL046W   0.7939252 0.2060748000
YIL072W   0.7397951 0.2602048891
YIR017C   0.9949457 0.0050543299
YIR034C   0.6754205 0.3245795009
YJL012C   0.2955978 0.7044021561
YJL106W   0.6071915 0.3928084516
YJL117W   0.6027921 0.3972079276
YJL153C   0.8663666 0.1336333982
YJL209W   0.7306424 0.2693576379
YJL211C   0.7306424 0.2693576379
YJL219W   0.5855291 0.4144709332
YJR010W   0.9756704 0.0243296370
YJR048W   0.6974343 0.3025657447
YJR073C   0.7418186 0.2581813529
YJR094C   0.7424569 0.2575431239
YJR137C   0.9145786 0.0854214494
YJR152W   0.6885893 0.3114107358
YKL001C   0.9628229 0.0371770941
YKL182W   0.4495741 0.5504259498
YKL216W   0.5894834 0.4105166029
YKR039W   0.5167480 0.4832520122
YKR048C   0.7582698 0.2417302121
YKR050W   0.7577054 0.2422946057
YKR069W   0.9892970 0.0107029578
YLR081W   0.8676022 0.1323978039
YLR142W   0.7976617 0.2023382532
YLR180W   0.6063393 0.3936606699
YLR263W   0.8525666 0.1474333553
YLR303W   0.6152230 0.3847770166
YLR329W   0.5083163 0.4916836936
YLR420W   0.8169901 0.1830099393
YLR438W   0.6309644 0.3690356436
YML051W   0.6910693 0.3089307489
YML054C   0.6768197 0.3231803495
YML075C   0.6383917 0.3616082569
YML121W   0.7988992 0.2011007582
YML123C   0.6660036 0.3339963640
YMR108W   0.2894995 0.7105004582
YMR133W   0.6918838 0.3081161741
YNL052W   0.4622968 0.5377032397
YNL061W   0.8131204 0.1868795885
YNL063W   0.7627565 0.2372435446
YNL064C   0.7899828 0.2100171630
YNL104C   0.5262872 0.4737128211
YNL142W   0.5028735 0.4971265336
YNL210W   0.7971262 0.2028737646
YNL241C   0.6142496 0.3857503979
YNL277W   0.9995843 0.0004157413
YNR001C   0.7333095 0.2666905424
YNR050C   0.7711793 0.2288207114
YOL006C   0.5265350 0.4734649827
YOR065W   0.7728634 0.2271365729
YOR120W   0.6428949 0.3571051017
YOR153W   0.6554547 0.3445453159
YOR328W   0.6542960 0.3457039562
YOR351C   0.5298196 0.4701803982
YOR375C   0.5737065 0.4262935001
YPL068C   0.3910023 0.6089977471
YPL111W   0.6500564 0.3499436084
YPL231W   0.6379082 0.3620918386
YPR065W   0.6440740 0.3559259697
YPR138C   0.6255829 0.3744170743
YPR145W   0.5636625 0.4363374639
YPR167C   0.5723779 0.4276220640

$permut.pc.stepwise.qda$best.pda$call
qda(x = data.training, grouping = labels.training, CV = loo, 
    na.action = na.omit)

$permut.pc.stepwise.qda$best.pda$training.label
  [1] CTL PHO CTL CTL PHO PHO CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL
 [19] CTL PHO PHO CTL CTL PHO CTL CTL CTL PHO PHO PHO PHO CTL CTL CTL CTL CTL
 [37] CTL PHO CTL CTL PHO PHO CTL CTL CTL PHO CTL CTL CTL CTL CTL PHO PHO CTL
 [55] PHO CTL PHO PHO CTL CTL CTL CTL PHO PHO CTL CTL CTL CTL PHO CTL PHO PHO
 [73] CTL CTL CTL CTL CTL CTL PHO CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL PHO
 [91] CTL CTL PHO PHO CTL CTL PHO CTL CTL PHO CTL CTL CTL CTL CTL PHO PHO PHO
[109] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL PHO
[127] CTL CTL PHO CTL CTL CTL PHO CTL CTL CTL PHO
Levels: CTL PHO

$permut.pc.stepwise.qda$best.pda$pda.method
[1] "qda"

$permut.pc.stepwise.qda$best.pda$loo
[1] TRUE

$permut.pc.stepwise.qda$best.pda$validation
[1] "LOO"

$permut.pc.stepwise.qda$best.pda$confusion
      true
object CTL PHO
   CTL  90  33
   PHO   6   8
attr(,"error")
[1] 0.2846715



$max.p
[1] 15

$errors
   stepwise.lda pc.stepwise.lda permut.stepwise.lda permut.pc.stepwise.lda
1    0.08029197      0.13138686           0.2977372              0.2964234
2    0.03649635      0.08029197           0.2961314              0.2936496
3    0.02189781      0.05839416           0.2945985              0.2913139
4    0.02189781      0.04379562           0.2934307              0.2896350
5    0.02189781      0.01459854           0.2929927              0.2895620
6    0.02189781      0.01459854           0.2935036              0.2897810
7    0.02919708      0.01459854           0.2940146              0.2904380
8    0.02919708      0.00729927           0.2950365              0.2918978
9    0.02919708      0.00729927           0.2975182              0.2938686
10   0.02189781      0.01459854           0.3003650              0.2994891
11   0.02189781      0.01459854           0.3062774              0.3048905
12   0.02919708      0.01459854           0.3114599              0.3112409
13   0.02919708      0.02189781           0.3189051              0.3212409
14   0.02919708      0.02919708           0.3296350              0.3303650
15   0.03649635      0.03649635           0.3445255              0.3457664
   stepwise.qda pc.stepwise.qda permut.stepwise.qda permut.pc.stepwise.qda
1    0.08029197      0.12408759           0.2994161              0.3002920
2    0.04379562      0.07299270           0.3062044              0.3067153
3    0.03649635      0.04379562           0.3187591              0.3145255
4    0.05109489      0.03649635           0.3311679              0.3280292
5    0.07299270      0.03649635           0.3471533              0.3389781
6    0.08029197      0.05839416           0.3597810              0.3519708
7    0.04379562      0.06569343           0.3702190              0.3659124
8    0.03649635      0.04379562           0.3813869              0.3749635
9    0.03649635      0.04379562           0.3872993              0.3854015
10   0.02919708      0.03649635           0.3956204              0.3918978
11   0.02919708      0.03649635           0.3991971              0.3968613
12   0.02919708      0.03649635           0.3945985              0.4023358
13   0.03649635      0.05839416           0.3970073              0.4010219
14   0.04379562      0.05109489           0.3956204              0.3973723
15   0.05109489      0.05109489           0.3912409              0.4009489

$legend.labels
[1] "LDA"                   "LDA with PC"           "LDA, permuted"        
[4] "LDA with PC, permuted" "QDA"                   "QDA with PC"          
[7] "QDA, permuted"         "QDA with PC, permuted"

$confusion.table
                        p      error CTL.CTL CTL.PHO PHO.CTL PHO.PHO
stepwise.lda           11 0.02189781      93       3       0      41
pc.stepwise.lda         9 0.00729927      95       1       0      41
permut.stepwise.lda     6 0.21897810      93       3      27      14
permut.pc.stepwise.lda  7 0.29927007      96       0      41       0
stepwise.qda           12 0.02919708      94       2       2      39
pc.stepwise.qda        12 0.03649635      94       2       3      38
permut.stepwise.qda     3 0.27737226      91       5      33       8
permut.pc.stepwise.qda  4 0.28467153      90       6      33       8

$best.errors
[1] 0.00729927

$best.vars
[1]  1  5  2  3  7  9 11 15 12

$best.method
[1] "pc.stepwise.lda"

$best.pda
$best.pda$max.p
[1] 15

$best.pda$errors
 [1] 0.13138686 0.08029197 0.05839416 0.04379562 0.01459854 0.01459854
 [7] 0.01459854 0.00729927 0.00729927 0.01459854 0.01459854 0.01459854
[13] 0.02189781 0.02919708 0.03649635

$best.pda$confusion.table
   step              error added.var added.var.name CTL.CTL CTL.PHO PHO.CTL
1     1  0.131386861313869         1         Comp.1      86      10       8
2     2 0.0802919708029197         5         Comp.5      88       8       3
3     3 0.0583941605839416         2         Comp.2      91       5       3
4     4 0.0437956204379562         3         Comp.3      91       5       1
5     5 0.0145985401459854         7         Comp.7      94       2       0
6     6 0.0145985401459854         9         Comp.9      94       2       0
7     7 0.0145985401459854        11        Comp.11      94       2       0
8     8 0.0072992700729927        15        Comp.15      95       1       0
9     9 0.0072992700729927        12        Comp.12      95       1       0
10   10 0.0145985401459854         6         Comp.6      94       2       0
11   11 0.0145985401459854        10        Comp.10      94       2       0
12   12 0.0145985401459854        14        Comp.14      94       2       0
13   13 0.0218978102189781        13        Comp.13      93       3       0
14   14 0.0291970802919708         8         Comp.8      93       3       1
15   15 0.0364963503649635         4         Comp.4      92       4       1
   PHO.PHO
1       33
2       38
3       38
4       40
5       41
6       41
7       41
8       41
9       41
10      41
11      41
12      41
13      41
14      40
15      40

$best.pda$best.pda
$best.pda$best.pda$class
  [1] PHO CTL PHO PHO PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL PHO CTL PHO PHO
 [19] CTL CTL CTL CTL CTL PHO CTL PHO PHO PHO CTL PHO CTL PHO PHO PHO CTL PHO
 [37] CTL PHO PHO CTL CTL PHO PHO PHO CTL PHO CTL CTL CTL PHO CTL CTL PHO CTL
 [55] CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL PHO PHO CTL PHO PHO
 [73] CTL CTL CTL CTL CTL PHO CTL PHO CTL PHO PHO CTL CTL CTL CTL CTL CTL CTL
 [91] CTL CTL CTL CTL PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[109] PHO PHO CTL CTL CTL PHO PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[127] CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL
Levels: CTL PHO

$best.pda$best.pda$posterior
                   CTL          PHO
YAL002W   1.180361e-03 9.988196e-01
YAL038W   8.543830e-01 1.456170e-01
YAR064W   3.071900e-01 6.928100e-01
YAR070C   2.994904e-06 9.999970e-01
YAR071W   7.387602e-06 9.999926e-01
YBL005W   9.999928e-01 7.235394e-06
YBL030C   9.999927e-01 7.281309e-06
YBR006W   9.999789e-01 2.114016e-05
YBR018C   9.999974e-01 2.644492e-06
YBR020W   9.999906e-01 9.406706e-06
YBR093C   3.191235e-06 9.999968e-01
YBR115C   9.999995e-01 5.315754e-07
YBR184W   9.999803e-01 1.965436e-05
YBR213W   9.999859e-01 1.408383e-05
YBR296C   2.156637e-07 9.999998e-01
YCL018W   9.999987e-01 1.312935e-06
YCR037C   6.959307e-03 9.930407e-01
YCR098C   1.662449e-04 9.998338e-01
YDL131W   9.995080e-01 4.919913e-04
YDL182W   9.792698e-01 2.073024e-02
YDL205C   9.999996e-01 3.943364e-07
YDL210W   9.999987e-01 1.345061e-06
YDR011W   9.999989e-01 1.077497e-06
YDR041W   1.461670e-03 9.985383e-01
YDR044W   9.999906e-01 9.442551e-06
YDR054C   4.078607e-03 9.959214e-01
YDR055W   1.387706e-02 9.861229e-01
YDR169C   1.182660e-06 9.999988e-01
YDR234W   9.999032e-01 9.678357e-05
YDR281C   2.878139e-04 9.997122e-01
YDR285W   9.999999e-01 1.024068e-07
YDR303C   9.250694e-03 9.907493e-01
YDR310C   6.596545e-04 9.993403e-01
YDR311W   7.962160e-04 9.992038e-01
YDR406W   9.999597e-01 4.031134e-05
YDR481C   3.825762e-01 6.174238e-01
YDR502C   9.999988e-01 1.172719e-06
YEL017C-A 1.278140e-04 9.998722e-01
YEL017W   1.420018e-03 9.985800e-01
YEL021W   9.999991e-01 9.083170e-07
YEL039C   9.999983e-01 1.650421e-06
YEL045C   4.102571e-03 9.958974e-01
YER017C   3.317710e-04 9.996682e-01
YER019W   6.553915e-04 9.993446e-01
YER026C   9.999415e-01 5.847682e-05
YER073W   3.055636e-04 9.996944e-01
YER086W   1.000000e+00 3.183466e-09
YER091C   9.975726e-01 2.427413e-03
YER179W   9.999996e-01 4.379567e-07
YFL004W   5.394447e-04 9.994606e-01
YFR030W   9.987494e-01 1.250570e-03
YGL009C   9.999999e-01 1.205600e-07
YGL073W   2.921445e-02 9.707855e-01
YGL213C   5.103417e-01 4.896583e-01
YGR019W   9.997126e-01 2.873944e-04
YGR044C   9.985419e-01 1.458125e-03
YGR088W   9.975697e-01 2.430290e-03
YGR121C   9.999727e-01 2.728126e-05
YGR157W   9.999966e-01 3.430057e-06
YGR233C   6.004864e-03 9.939951e-01
YGR281W   9.997374e-01 2.626383e-04
YHL022C   9.999999e-01 5.829156e-08
YHL036W   9.984125e-01 1.587525e-03
YHR007C   9.997785e-01 2.214538e-04
YHR008C   9.999339e-01 6.612861e-05
YHR014W   9.999787e-01 2.125697e-05
YHR037W   9.791076e-01 2.089245e-02
YHR136C   3.694645e-03 9.963054e-01
YHR137W   3.782415e-03 9.962176e-01
YHR153C   9.998465e-01 1.534510e-04
YHR168W   1.542028e-06 9.999985e-01
YHR215W   7.387602e-06 9.999926e-01
YIL015W   9.999990e-01 1.015342e-06
YIL046W   5.950197e-01 4.049803e-01
YIL072W   9.999984e-01 1.617301e-06
YIR017C   9.999567e-01 4.329454e-05
YIR034C   5.462245e-01 4.537755e-01
YJL012C   5.945531e-05 9.999405e-01
YJL106W   9.999049e-01 9.507339e-05
YJL117W   6.821693e-03 9.931783e-01
YJL153C   9.999944e-01 5.649777e-06
YJL209W   9.103897e-03 9.908961e-01
YJL211C   9.103897e-03 9.908961e-01
YJL219W   9.875009e-01 1.249908e-02
YJR010W   9.999977e-01 2.334443e-06
YJR048W   9.999720e-01 2.801035e-05
YJR073C   8.846898e-01 1.153102e-01
YJR094C   9.980539e-01 1.946055e-03
YJR137C   8.562330e-01 1.437670e-01
YJR152W   9.990810e-01 9.190066e-04
YKL001C   9.998944e-01 1.055984e-04
YKL182W   9.999984e-01 1.573320e-06
YKL216W   9.999868e-01 1.320916e-05
YKR039W   9.999997e-01 2.586475e-07
YKR048C   2.843099e-03 9.971569e-01
YKR050W   2.765633e-03 9.972344e-01
YKR069W   8.512199e-01 1.487801e-01
YLR081W   9.999603e-01 3.965565e-05
YLR142W   9.999720e-01 2.804877e-05
YLR180W   9.994980e-01 5.020017e-04
YLR263W   1.000000e+00 3.561829e-08
YLR303W   9.998574e-01 1.425710e-04
YLR329W   9.995704e-01 4.296344e-04
YLR420W   9.997158e-01 2.842057e-04
YLR438W   9.931149e-01 6.885124e-03
YML051W   9.999977e-01 2.251836e-06
YML054C   6.141926e-01 3.858074e-01
YML075C   9.999874e-01 1.264866e-05
YML121W   4.308572e-03 9.956914e-01
YML123C   1.804060e-12 1.000000e+00
YMR108W   9.992875e-01 7.124524e-04
YMR133W   1.000000e+00 1.161215e-08
YNL052W   9.999886e-01 1.143485e-05
YNL061W   2.985695e-03 9.970143e-01
YNL063W   1.804604e-03 9.981954e-01
YNL064C   7.825465e-04 9.992175e-01
YNL104C   8.791805e-01 1.208195e-01
YNL142W   9.999989e-01 1.053577e-06
YNL210W   9.999997e-01 2.613665e-07
YNL241C   9.999904e-01 9.583206e-06
YNL277W   9.995116e-01 4.883835e-04
YNR001C   9.999994e-01 5.839369e-07
YNR050C   9.811485e-01 1.885152e-02
YOL006C   9.997514e-01 2.486431e-04
YOR065W   9.360998e-01 6.390021e-02
YOR120W   9.999999e-01 6.369000e-08
YOR153W   9.996168e-01 3.831822e-04
YOR328W   9.998523e-01 1.477410e-04
YOR351C   9.999990e-01 1.009612e-06
YOR375C   9.992742e-01 7.258319e-04
YPL068C   4.415335e-04 9.995585e-01
YPL111W   9.999963e-01 3.684181e-06
YPL231W   9.950837e-01 4.916314e-03
YPR065W   9.999991e-01 9.464344e-07
YPR138C   9.999980e-01 1.992038e-06
YPR145W   9.878468e-01 1.215325e-02
YPR167C   9.999477e-01 5.232916e-05

$best.pda$best.pda$call
lda(x = data.training, grouping = labels.training, CV = loo, 
    na.action = na.omit)

$best.pda$best.pda$training.names
  [1] "YAL002W"   "YAL038W"   "YAR064W"   "YAR070C"   "YAR071W"   "YBL005W"  
  [7] "YBL030C"   "YBR006W"   "YBR018C"   "YBR020W"   "YBR093C"   "YBR115C"  
 [13] "YBR184W"   "YBR213W"   "YBR296C"   "YCL018W"   "YCR037C"   "YCR098C"  
 [19] "YDL131W"   "YDL182W"   "YDL205C"   "YDL210W"   "YDR011W"   "YDR041W"  
 [25] "YDR044W"   "YDR054C"   "YDR055W"   "YDR169C"   "YDR234W"   "YDR281C"  
 [31] "YDR285W"   "YDR303C"   "YDR310C"   "YDR311W"   "YDR406W"   "YDR481C"  
 [37] "YDR502C"   "YEL017C-A" "YEL017W"   "YEL021W"   "YEL039C"   "YEL045C"  
 [43] "YER017C"   "YER019W"   "YER026C"   "YER073W"   "YER086W"   "YER091C"  
 [49] "YER179W"   "YFL004W"   "YFR030W"   "YGL009C"   "YGL073W"   "YGL213C"  
 [55] "YGR019W"   "YGR044C"   "YGR088W"   "YGR121C"   "YGR157W"   "YGR233C"  
 [61] "YGR281W"   "YHL022C"   "YHL036W"   "YHR007C"   "YHR008C"   "YHR014W"  
 [67] "YHR037W"   "YHR136C"   "YHR137W"   "YHR153C"   "YHR168W"   "YHR215W"  
 [73] "YIL015W"   "YIL046W"   "YIL072W"   "YIR017C"   "YIR034C"   "YJL012C"  
 [79] "YJL106W"   "YJL117W"   "YJL153C"   "YJL209W"   "YJL211C"   "YJL219W"  
 [85] "YJR010W"   "YJR048W"   "YJR073C"   "YJR094C"   "YJR137C"   "YJR152W"  
 [91] "YKL001C"   "YKL182W"   "YKL216W"   "YKR039W"   "YKR048C"   "YKR050W"  
 [97] "YKR069W"   "YLR081W"   "YLR142W"   "YLR180W"   "YLR263W"   "YLR303W"  
[103] "YLR329W"   "YLR420W"   "YLR438W"   "YML051W"   "YML054C"   "YML075C"  
[109] "YML121W"   "YML123C"   "YMR108W"   "YMR133W"   "YNL052W"   "YNL061W"  
[115] "YNL063W"   "YNL064C"   "YNL104C"   "YNL142W"   "YNL210W"   "YNL241C"  
[121] "YNL277W"   "YNR001C"   "YNR050C"   "YOL006C"   "YOR065W"   "YOR120W"  
[127] "YOR153W"   "YOR328W"   "YOR351C"   "YOR375C"   "YPL068C"   "YPL111W"  
[133] "YPL231W"   "YPR065W"   "YPR138C"   "YPR145W"   "YPR167C"  

$best.pda$best.pda$training.label
  [1] PHO CTL PHO PHO PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL PHO CTL PHO PHO
 [19] CTL CTL CTL CTL CTL PHO CTL PHO PHO PHO CTL PHO CTL PHO PHO PHO CTL PHO
 [37] CTL PHO PHO CTL CTL PHO PHO PHO CTL PHO CTL CTL CTL PHO CTL CTL CTL CTL
 [55] CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL PHO PHO CTL PHO PHO
 [73] CTL CTL CTL CTL CTL PHO CTL PHO CTL PHO PHO CTL CTL CTL CTL CTL CTL CTL
 [91] CTL CTL CTL CTL PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[109] PHO PHO CTL CTL CTL PHO PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[127] CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL
Levels: CTL PHO

$best.pda$best.pda$pda.method
[1] "lda"

$best.pda$best.pda$loo
[1] TRUE

$best.pda$best.pda$validation
[1] "LOO"

$best.pda$best.pda$confusion
      true
object CTL PHO
   CTL  95   0
   PHO   1  41
attr(,"error")
[1] 0.00729927


$best.pda$best.p
[1] 9

$best.pda$best.vars
[1]  1  5  2  3  7  9 11 15 12

$best.pda$best.var.names
[1] "Comp.1"  "Comp.5"  "Comp.2"  "Comp.3"  "Comp.7"  "Comp.9"  "Comp.11"
[8] "Comp.15" "Comp.12"

$best.pda$best.error
[1] 0.00729927

$best.pda$pc.transform
[1] TRUE

$best.pda$var.order
 [1]  1  5  2  3  7  9 11 15 12  6 10 14 13  8  4


