$stepwise.lda
$stepwise.lda$max.p
[1] 8

$stepwise.lda$errors
[1] 0.02272727 0.01136364 0.01136364 0.02272727 0.02272727 0.02272727 0.02272727
[8] 0.02272727

$stepwise.lda$confusion.table
  step              error added.var                      added.var.name CTL.CTL
1    1 0.0227272727272727         1 Low.Pi_vs_High.Pi_in_WT_.NBW7._exp1      80
2    2 0.0113636363636364         5                         pho80_vs_WT      80
3    3 0.0113636363636364         2 Low.Pi_vs_High.Pi_in_WT_.NBW7._exp2      80
4    4 0.0227272727272727         3   Low.Pi_vs_High.Pi_in_WT_.DBY7286.      80
5    5 0.0227272727272727         4                         PHO4c_vs_WT      80
6    6 0.0227272727272727         6                         pho85_vs_WT      80
7    7 0.0227272727272727         7                   PHO81c_vs_WT_exp1      80
8    8 0.0227272727272727         8                   PHO81c_vs_WT_exp2      80
  CTL.PHO PHO.CTL PHO.PHO
1       0       2       6
2       0       1       7
3       0       1       7
4       0       2       6
5       0       2       6
6       0       2       6
7       0       2       6
8       0       2       6

$stepwise.lda$best.pda
$stepwise.lda$best.pda$class
 [1] CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[20] CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[39] CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[58] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[77] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
Levels: CTL PHO

$stepwise.lda$best.pda$posterior
                 CTL          PHO
YAL038W 9.999903e-01 9.699651e-06
YAR071W 8.314360e-13 1.000000e+00
YBL005W 9.999988e-01 1.181800e-06
YBL030C 9.999887e-01 1.127009e-05
YBR006W 9.999997e-01 3.077050e-07
YBR018C 1.000000e+00 4.844014e-09
YBR020W 1.000000e+00 7.091282e-09
YBR093C 1.248449e-08 1.000000e+00
YBR115C 9.999718e-01 2.816701e-05
YBR184W 9.999997e-01 3.072343e-07
YBR296C 4.281576e-05 9.999572e-01
YCL018W 9.999989e-01 1.084210e-06
YDL131W 9.999899e-01 1.006793e-05
YDL182W 9.999998e-01 1.846237e-07
YDL205C 9.999604e-01 3.957552e-05
YDL210W 1.000000e+00 2.831793e-09
YDR011W 9.999995e-01 4.960685e-07
YDR044W 9.999813e-01 1.874503e-05
YDR234W 9.999997e-01 3.254264e-07
YDR285W 1.000000e+00 6.258363e-09
YDR406W 9.999473e-01 5.268268e-05
YDR481C 2.200900e-01 7.799100e-01
YEL021W 9.999997e-01 2.994953e-07
YEL039C 9.999982e-01 1.786563e-06
YER026C 9.999998e-01 2.419350e-07
YER086W 9.999877e-01 1.228879e-05
YER179W 1.000000e+00 3.674796e-08
YGL009C 9.999999e-01 1.487919e-07
YGL073W 9.999998e-01 1.843317e-07
YGL213C 9.999993e-01 7.444542e-07
YGR019W 9.999994e-01 6.056626e-07
YGR044C 9.999991e-01 9.301657e-07
YGR088W 9.999994e-01 6.416167e-07
YGR121C 9.999996e-01 3.574032e-07
YGR157W 9.999991e-01 9.005669e-07
YGR233C 9.999999e-01 6.031587e-08
YGR281W 9.999509e-01 4.905170e-05
YHL022C 1.000000e+00 1.180719e-12
YHR007C 1.000000e+00 5.628900e-09
YHR008C 9.999977e-01 2.290222e-06
YHR014W 1.000000e+00 2.284793e-13
YHR037W 1.000000e+00 2.510164e-09
YHR136C 2.677966e-04 9.997322e-01
YHR153C 1.000000e+00 2.458479e-08
YIL015W 1.000000e+00 3.852989e-09
YIL072W 9.999990e-01 1.030372e-06
YIR034C 9.999301e-01 6.988400e-05
YJL106W 9.999999e-01 6.792651e-08
YJL117W 2.213877e-01 7.786123e-01
YJL153C 9.999948e-01 5.216890e-06
YJL219W 1.000000e+00 4.573466e-08
YJR048W 9.999991e-01 8.776323e-07
YJR073C 1.000000e+00 1.390449e-08
YJR094C 1.000000e+00 3.437138e-09
YJR152W 9.999999e-01 1.252817e-07
YKL182W 9.999990e-01 9.696311e-07
YKL216W 9.999995e-01 5.476115e-07
YKR039W 9.999999e-01 8.159330e-08
YLR081W 9.999830e-01 1.696514e-05
YLR142W 9.976662e-01 2.333812e-03
YLR263W 1.000000e+00 8.274063e-09
YLR329W 1.000000e+00 5.446114e-09
YLR420W 9.999989e-01 1.105357e-06
YLR438W 9.999997e-01 2.686162e-07
YML051W 9.999993e-01 7.497552e-07
YML054C 1.000000e+00 1.341231e-09
YML075C 9.999987e-01 1.295556e-06
YML123C 4.781575e-14 1.000000e+00
YMR108W 1.000000e+00 9.214187e-09
YMR133W 1.000000e+00 1.138751e-08
YNL052W 9.999979e-01 2.087206e-06
YNL104C 9.999800e-01 1.995405e-05
YNL142W 1.000000e+00 5.756135e-09
YNL210W 1.000000e+00 2.707138e-08
YNR001C 9.998591e-01 1.409030e-04
YNR050C 1.000000e+00 4.112449e-08
YOL006C 9.999996e-01 4.294339e-07
YOR065W 9.999994e-01 5.613023e-07
YOR120W 9.999999e-01 9.944845e-08
YOR153W 9.987647e-01 1.235309e-03
YOR328W 9.999993e-01 7.008550e-07
YOR351C 1.000000e+00 6.615833e-12
YOR375C 9.999990e-01 9.669330e-07
YPL111W 9.999996e-01 4.189593e-07
YPL231W 9.999989e-01 1.104782e-06
YPR065W 1.000000e+00 3.924103e-10
YPR138C 1.000000e+00 3.280658e-08
YPR145W 9.999998e-01 1.877432e-07

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

$stepwise.lda$best.pda$training.names
 [1] "YAL038W" "YAR071W" "YBL005W" "YBL030C" "YBR006W" "YBR018C" "YBR020W"
 [8] "YBR093C" "YBR115C" "YBR184W" "YBR296C" "YCL018W" "YDL131W" "YDL182W"
[15] "YDL205C" "YDL210W" "YDR011W" "YDR044W" "YDR234W" "YDR285W" "YDR406W"
[22] "YDR481C" "YEL021W" "YEL039C" "YER026C" "YER086W" "YER179W" "YGL009C"
[29] "YGL073W" "YGL213C" "YGR019W" "YGR044C" "YGR088W" "YGR121C" "YGR157W"
[36] "YGR233C" "YGR281W" "YHL022C" "YHR007C" "YHR008C" "YHR014W" "YHR037W"
[43] "YHR136C" "YHR153C" "YIL015W" "YIL072W" "YIR034C" "YJL106W" "YJL117W"
[50] "YJL153C" "YJL219W" "YJR048W" "YJR073C" "YJR094C" "YJR152W" "YKL182W"
[57] "YKL216W" "YKR039W" "YLR081W" "YLR142W" "YLR263W" "YLR329W" "YLR420W"
[64] "YLR438W" "YML051W" "YML054C" "YML075C" "YML123C" "YMR108W" "YMR133W"
[71] "YNL052W" "YNL104C" "YNL142W" "YNL210W" "YNR001C" "YNR050C" "YOL006C"
[78] "YOR065W" "YOR120W" "YOR153W" "YOR328W" "YOR351C" "YOR375C" "YPL111W"
[85] "YPL231W" "YPR065W" "YPR138C" "YPR145W"

$stepwise.lda$best.pda$training.label
 [1] CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[20] CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL
[39] CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[58] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[77] CTL CTL CTL CTL CTL CTL 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  80   1
   PHO   0   7
attr(,"error")
[1] 0.01136364


$stepwise.lda$best.p
[1] 3

$stepwise.lda$best.vars
[1] 1 5 2

$stepwise.lda$best.var.names
[1] "Low.Pi_vs_High.Pi_in_WT_.NBW7._exp1" "pho80_vs_WT"                        
[3] "Low.Pi_vs_High.Pi_in_WT_.NBW7._exp2"

$stepwise.lda$best.error
[1] 0.01136364

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

$stepwise.lda$var.order
[1] 1 5 2 3 4 6 7 8


$pc.stepwise.lda
$pc.stepwise.lda$max.p
[1] 8

$pc.stepwise.lda$errors
[1] 0.02272727 0.02272727 0.02272727 0.02272727 0.02272727 0.02272727 0.02272727
[8] 0.02272727

$pc.stepwise.lda$confusion.table
  step              error added.var added.var.name CTL.CTL CTL.PHO PHO.CTL
1    1 0.0227272727272727         1         Comp.1      80       0       2
2    2 0.0227272727272727         2         Comp.2      80       0       2
3    3 0.0227272727272727         3         Comp.3      80       0       2
4    4 0.0227272727272727         4         Comp.4      80       0       2
5    5 0.0227272727272727         5         Comp.5      80       0       2
6    6 0.0227272727272727         6         Comp.6      80       0       2
7    7 0.0227272727272727         7         Comp.7      80       0       2
8    8 0.0227272727272727         8         Comp.8      80       0       2
  PHO.PHO
1       6
2       6
3       6
4       6
5       6
6       6
7       6
8       6

$pc.stepwise.lda$best.pda
$pc.stepwise.lda$best.pda$class
 [1] CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[20] CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[39] CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[58] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[77] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
Levels: CTL PHO

$pc.stepwise.lda$best.pda$posterior
                 CTL          PHO
YAL038W 1.000000e+00 3.149348e-09
YAR071W 4.776055e-17 1.000000e+00
YBL005W 1.000000e+00 3.650175e-09
YBL030C 1.000000e+00 2.427811e-08
YBR006W 1.000000e+00 2.631645e-09
YBR018C 1.000000e+00 2.551971e-11
YBR020W 1.000000e+00 2.597740e-10
YBR093C 6.977080e-14 1.000000e+00
YBR115C 1.000000e+00 2.371966e-08
YBR184W 1.000000e+00 2.388355e-11
YBR296C 2.007969e-12 1.000000e+00
YCL018W 1.000000e+00 6.829122e-09
YDL131W 1.000000e+00 2.983790e-09
YDL182W 1.000000e+00 1.402669e-11
YDL205C 1.000000e+00 1.834979e-12
YDL210W 1.000000e+00 6.552504e-13
YDR011W 1.000000e+00 9.866790e-13
YDR044W 1.000000e+00 3.802711e-09
YDR234W 1.000000e+00 9.463858e-11
YDR285W 1.000000e+00 1.014640e-09
YDR406W 9.999998e-01 2.408822e-07
YDR481C 1.181889e-01 8.818111e-01
YEL021W 1.000000e+00 3.317068e-13
YEL039C 1.000000e+00 2.222499e-10
YER026C 1.000000e+00 1.727885e-10
YER086W 1.000000e+00 1.625322e-09
YER179W 1.000000e+00 1.075699e-09
YGL009C 1.000000e+00 6.628625e-09
YGL073W 1.000000e+00 5.495392e-12
YGL213C 1.000000e+00 9.368972e-12
YGR019W 1.000000e+00 2.537559e-10
YGR044C 1.000000e+00 1.507399e-10
YGR088W 1.000000e+00 3.217814e-09
YGR121C 1.000000e+00 1.012258e-09
YGR157W 1.000000e+00 6.179792e-10
YGR233C 1.000000e+00 1.335852e-11
YGR281W 1.000000e+00 1.561544e-08
YHL022C 1.000000e+00 8.190735e-15
YHR007C 1.000000e+00 5.875554e-11
YHR008C 1.000000e+00 1.070334e-08
YHR014W 1.000000e+00 3.973630e-14
YHR037W 1.000000e+00 4.440212e-13
YHR136C 7.518603e-13 1.000000e+00
YHR153C 1.000000e+00 1.766186e-11
YIL015W 1.000000e+00 1.068168e-13
YIL072W 1.000000e+00 8.474478e-09
YIR034C 9.999827e-01 1.732816e-05
YJL106W 1.000000e+00 4.926060e-11
YJL117W 9.873566e-01 1.264344e-02
YJL153C 9.999999e-01 1.148318e-07
YJL219W 1.000000e+00 1.254912e-11
YJR048W 1.000000e+00 2.135145e-10
YJR073C 1.000000e+00 1.216986e-10
YJR094C 1.000000e+00 8.523489e-13
YJR152W 9.999997e-01 3.054651e-07
YKL182W 1.000000e+00 4.484524e-11
YKL216W 1.000000e+00 4.333342e-12
YKR039W 1.000000e+00 3.232315e-10
YLR081W 1.000000e+00 4.566523e-10
YLR142W 1.000000e+00 3.028190e-09
YLR263W 1.000000e+00 7.036034e-11
YLR329W 1.000000e+00 2.856925e-13
YLR420W 1.000000e+00 2.417092e-11
YLR438W 9.999999e-01 9.696124e-08
YML051W 1.000000e+00 8.919086e-10
YML054C 1.000000e+00 7.901072e-11
YML075C 1.000000e+00 1.712892e-10
YML123C 5.581078e-18 1.000000e+00
YMR108W 1.000000e+00 9.898362e-13
YMR133W 1.000000e+00 1.018499e-11
YNL052W 1.000000e+00 1.910774e-10
YNL104C 1.000000e+00 2.245356e-09
YNL142W 1.000000e+00 2.423296e-11
YNL210W 1.000000e+00 8.734343e-11
YNR001C 9.999991e-01 9.145955e-07
YNR050C 1.000000e+00 1.924233e-08
YOL006C 1.000000e+00 9.224258e-12
YOR065W 1.000000e+00 3.522610e-09
YOR120W 9.999999e-01 9.432583e-08
YOR153W 1.000000e+00 1.369913e-09
YOR328W 1.000000e+00 2.322348e-10
YOR351C 1.000000e+00 1.051197e-12
YOR375C 1.000000e+00 4.006881e-10
YPL111W 1.000000e+00 5.608772e-13
YPL231W 1.000000e+00 1.117806e-10
YPR065W 1.000000e+00 5.939356e-12
YPR138C 1.000000e+00 1.092633e-10
YPR145W 1.000000e+00 9.151387e-12

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

$pc.stepwise.lda$best.pda$training.names
 [1] "YAL038W" "YAR071W" "YBL005W" "YBL030C" "YBR006W" "YBR018C" "YBR020W"
 [8] "YBR093C" "YBR115C" "YBR184W" "YBR296C" "YCL018W" "YDL131W" "YDL182W"
[15] "YDL205C" "YDL210W" "YDR011W" "YDR044W" "YDR234W" "YDR285W" "YDR406W"
[22] "YDR481C" "YEL021W" "YEL039C" "YER026C" "YER086W" "YER179W" "YGL009C"
[29] "YGL073W" "YGL213C" "YGR019W" "YGR044C" "YGR088W" "YGR121C" "YGR157W"
[36] "YGR233C" "YGR281W" "YHL022C" "YHR007C" "YHR008C" "YHR014W" "YHR037W"
[43] "YHR136C" "YHR153C" "YIL015W" "YIL072W" "YIR034C" "YJL106W" "YJL117W"
[50] "YJL153C" "YJL219W" "YJR048W" "YJR073C" "YJR094C" "YJR152W" "YKL182W"
[57] "YKL216W" "YKR039W" "YLR081W" "YLR142W" "YLR263W" "YLR329W" "YLR420W"
[64] "YLR438W" "YML051W" "YML054C" "YML075C" "YML123C" "YMR108W" "YMR133W"
[71] "YNL052W" "YNL104C" "YNL142W" "YNL210W" "YNR001C" "YNR050C" "YOL006C"
[78] "YOR065W" "YOR120W" "YOR153W" "YOR328W" "YOR351C" "YOR375C" "YPL111W"
[85] "YPL231W" "YPR065W" "YPR138C" "YPR145W"

$pc.stepwise.lda$best.pda$training.label
 [1] CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[20] CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL
[39] CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[58] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[77] CTL CTL CTL CTL CTL CTL 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  80   2
   PHO   0   6
attr(,"error")
[1] 0.02272727


$pc.stepwise.lda$best.p
[1] 8

$pc.stepwise.lda$best.vars
[1] 1 2 3 4 5 6 7 8

$pc.stepwise.lda$best.var.names
[1] "Comp.1" "Comp.2" "Comp.3" "Comp.4" "Comp.5" "Comp.6" "Comp.7" "Comp.8"

$pc.stepwise.lda$best.error
[1] 0.02272727

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

$pc.stepwise.lda$var.order
[1] 1 2 3 4 5 6 7 8


$permut.stepwise.lda
$permut.stepwise.lda$errors
    permut.1  permut.2  permut.3  permut.4  permut.5  permut.6  permut.7
1 0.09090909 0.0909091 0.0909091 0.0909091 0.0909091 0.0909091 0.0909091
2 0.09090909 0.0909091 0.0909091 0.0909091 0.0909091 0.0909091 0.0909091
3 0.09090909 0.0909091 0.0909091 0.0909091 0.0909091 0.0909091 0.0909091
4 0.09090909 0.0909091 0.0909091 0.1022727 0.0909091 0.0909091 0.0909091
5 0.09090909 0.0909091 0.0909091 0.1136364 0.1022727 0.0909091 0.0909091
6 0.07954545 0.0909091 0.0909091 0.1136364 0.1022727 0.0909091 0.0909091
7 0.09090909 0.1022727 0.0909091 0.1250000 0.1136364 0.1022727 0.0909091
8 0.09090909 0.1250000 0.0909091 0.1363636 0.1022727 0.1136364 0.1136364
    permut.8  permut.9 permut.10   err.mean      err.sd   err.sterr
1 0.09090909 0.0909091 0.0909091 0.09090909 0.000000000 0.000000000
2 0.09090909 0.0909091 0.0909091 0.09090909 0.000000000 0.000000000
3 0.09090909 0.0909091 0.0909091 0.09090909 0.000000000 0.000000000
4 0.09090909 0.1022727 0.0909091 0.09318182 0.004791330 0.001515152
5 0.09090909 0.1022727 0.0909091 0.09545455 0.007945522 0.002512595
6 0.07954545 0.1136364 0.0909091 0.09431818 0.012038067 0.003806771
7 0.07954545 0.1136364 0.1022727 0.10113636 0.013604761 0.004302203
8 0.09090909 0.1250000 0.1022727 0.10909091 0.016248190 0.005138129

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

$permut.stepwise.lda$best.error
[1] 0.0909091

$permut.stepwise.lda$best.pda
$permut.stepwise.lda$best.pda$class
 [1] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[20] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[39] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[58] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[77] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
Levels: CTL PHO

$permut.stepwise.lda$best.pda$posterior
              CTL        PHO
YAL038W 0.8348090 0.16519102
YAR071W 0.9816701 0.01832990
YBL005W 0.9280619 0.07193809
YBL030C 0.8794957 0.12050427
YBR006W 0.9253505 0.07464948
YBR018C 0.8746144 0.12538559
YBR020W 0.9758214 0.02417859
YBR093C 0.5597677 0.44023228
YBR115C 0.9542856 0.04571436
YBR184W 0.9188572 0.08114277
YBR296C 0.8310902 0.16890975
YCL018W 0.9412776 0.05872240
YDL131W 0.8890308 0.11096915
YDL182W 0.8992612 0.10073880
YDL205C 0.8897456 0.11025440
YDL210W 0.9275823 0.07241771
YDR011W 0.9194213 0.08057875
YDR044W 0.7639337 0.23606626
YDR234W 0.9523748 0.04762518
YDR285W 0.9720182 0.02798179
YDR406W 0.8756883 0.12431169
YDR481C 0.8357887 0.16421135
YEL021W 0.8712928 0.12870715
YEL039C 0.8418738 0.15812621
YER026C 0.9011730 0.09882701
YER086W 0.8697254 0.13027464
YER179W 0.9419728 0.05802716
YGL009C 0.9625133 0.03748665
YGL073W 0.8965477 0.10345229
YGL213C 0.8713423 0.12865767
YGR019W 0.9437977 0.05620227
YGR044C 0.9316283 0.06837165
YGR088W 0.9370852 0.06291480
YGR121C 0.9414449 0.05855512
YGR157W 0.9005372 0.09946285
YGR233C 0.9238138 0.07618624
YGR281W 0.8435724 0.15642765
YHL022C 0.9732763 0.02672372
YHR007C 0.9512989 0.04870109
YHR008C 0.9308533 0.06914673
YHR014W 0.9820709 0.01792910
YHR037W 0.9615022 0.03849778
YHR136C 0.9237254 0.07627459
YHR153C 0.9487298 0.05127018
YIL015W 0.8976949 0.10230509
YIL072W 0.9500204 0.04997961
YIR034C 0.9262325 0.07376754
YJL106W 0.8713834 0.12861657
YJL117W 0.8093844 0.19061559
YJL153C 0.9327174 0.06728261
YJL219W 0.9363868 0.06361320
YJR048W 0.8485743 0.15142571
YJR073C 0.9100399 0.08996010
YJR094C 0.9299098 0.07009018
YJR152W 0.9544619 0.04553811
YKL182W 0.9358069 0.06419312
YKL216W 0.8833746 0.11662543
YKR039W 0.9247087 0.07529133
YLR081W 0.8836940 0.11630599
YLR142W 0.8631790 0.13682105
YLR263W 0.9867948 0.01320519
YLR329W 0.9067613 0.09323873
YLR420W 0.9077179 0.09228209
YLR438W 0.9398495 0.06015055
YML051W 0.8879093 0.11209066
YML054C 0.9586431 0.04135692
YML075C 0.9191121 0.08088791
YML123C 0.5479540 0.45204603
YMR108W 0.9388789 0.06112108
YMR133W 0.9295176 0.07048241
YNL052W 0.8536886 0.14631142
YNL104C 0.8340458 0.16595424
YNL142W 0.9675668 0.03243315
YNL210W 0.9503749 0.04962511
YNR001C 0.7787976 0.22120240
YNR050C 0.9661396 0.03386041
YOL006C 0.9228107 0.07718934
YOR065W 0.9104187 0.08958126
YOR120W 0.9484599 0.05154013
YOR153W 0.8612006 0.13879936
YOR328W 0.9366380 0.06336201
YOR351C 0.9792424 0.02075761
YOR375C 0.9547421 0.04525790
YPL111W 0.9028295 0.09717049
YPL231W 0.8937059 0.10629406
YPR065W 0.9589651 0.04103489
YPR138C 0.9873028 0.01269718
YPR145W 0.8977420 0.10225804

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

$permut.stepwise.lda$best.pda$training.label
 [1] CTL PHO CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL
[20] CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[39] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL
[58] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[77] CTL CTL CTL PHO CTL CTL PHO CTL CTL CTL PHO 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  80   8
   PHO   0   0
attr(,"error")
[1] 0.0909091



$permut.pc.stepwise.lda
$permut.pc.stepwise.lda$errors
   permut.1  permut.2  permut.3  permut.4  permut.5  permut.6  permut.7
1 0.0909091 0.0909091 0.0909091 0.0909091 0.0909091 0.0909091 0.0909091
2 0.0909091 0.0909091 0.0909091 0.0909091 0.0909091 0.0909091 0.0909091
3 0.0909091 0.0909091 0.0909091 0.0909091 0.0909091 0.0909091 0.0909091
4 0.0909091 0.0909091 0.0909091 0.0909091 0.0909091 0.0909091 0.0909091
5 0.0909091 0.0909091 0.0909091 0.0909091 0.0909091 0.0909091 0.0909091
6 0.0909091 0.0909091 0.0909091 0.0909091 0.0909091 0.0909091 0.1022727
7 0.0909091 0.0909091 0.0909091 0.1022727 0.0909091 0.1022727 0.1022727
8 0.1022727 0.0909091 0.1022727 0.1022727 0.1022727 0.1022727 0.1022727
   permut.8  permut.9 permut.10   err.mean      err.sd   err.sterr
1 0.0909091 0.0909091 0.0909091 0.09090909 0.000000000 0.000000000
2 0.0909091 0.0909091 0.0909091 0.09090909 0.000000000 0.000000000
3 0.0909091 0.0909091 0.0909091 0.09090909 0.000000000 0.000000000
4 0.0909091 0.0909091 0.0909091 0.09090909 0.000000000 0.000000000
5 0.0909091 0.0909091 0.0909091 0.09090909 0.000000000 0.000000000
6 0.0909091 0.0909091 0.0909091 0.09204545 0.003593497 0.001136364
7 0.0909091 0.0909091 0.0909091 0.09431818 0.005489158 0.001735824
8 0.1022727 0.0909091 0.0909091 0.09886364 0.005489158 0.001735824

$permut.pc.stepwise.lda$best.p
[1] 8

$permut.pc.stepwise.lda$best.error
[1] 0.0909091

$permut.pc.stepwise.lda$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 CTL
[20] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[39] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[58] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[77] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
Levels: CTL PHO

$permut.pc.stepwise.lda$best.pda$posterior
              CTL          PHO
YAL038W 0.7318282 0.2681717795
YAR071W 0.9797627 0.0202373471
YBL005W 0.9457076 0.0542924025
YBL030C 0.9808711 0.0191288658
YBR006W 0.9636074 0.0363925996
YBR018C 0.9838292 0.0161708364
YBR020W 0.9804159 0.0195841389
YBR093C 0.9892433 0.0107566816
YBR115C 0.9893931 0.0106069214
YBR184W 0.9442608 0.0557392468
YBR296C 0.9994850 0.0005150461
YCL018W 0.9418439 0.0581561116
YDL131W 0.9459159 0.0540841244
YDL182W 0.9207331 0.0792668984
YDL205C 0.9957367 0.0042632624
YDL210W 0.9370372 0.0629628094
YDR011W 0.9635654 0.0364346022
YDR044W 0.8394597 0.1605403342
YDR234W 0.9757429 0.0242571409
YDR285W 0.9917387 0.0082613233
YDR406W 0.9117113 0.0882886953
YDR481C 0.9676092 0.0323908241
YEL021W 0.8242563 0.1757437313
YEL039C 0.8794008 0.1205992214
YER026C 0.9016021 0.0983979063
YER086W 0.8655008 0.1344992196
YER179W 0.9790842 0.0209157990
YGL009C 0.9295668 0.0704331983
YGL073W 0.8874282 0.1125717795
YGL213C 0.7597006 0.2402994122
YGR019W 0.8913693 0.1086306836
YGR044C 0.9352739 0.0647261412
YGR088W 0.7416752 0.2583248293
YGR121C 0.9689602 0.0310398396
YGR157W 0.9149460 0.0850540245
YGR233C 0.9739886 0.0260114086
YGR281W 0.8066830 0.1933170439
YHL022C 0.9738995 0.0261004702
YHR007C 0.9684845 0.0315154842
YHR008C 0.9444285 0.0555715267
YHR014W 0.9872723 0.0127276971
YHR037W 0.9702131 0.0297868889
YHR136C 0.9986553 0.0013446573
YHR153C 0.9433661 0.0566338603
YIL015W 0.8949262 0.1050737858
YIL072W 0.9846783 0.0153216558
YIR034C 0.9849581 0.0150419083
YJL106W 0.9152875 0.0847124725
YJL117W 0.9452137 0.0547862952
YJL153C 0.9201931 0.0798068707
YJL219W 0.9748415 0.0251585493
YJR048W 0.6811003 0.3188996944
YJR073C 0.9475334 0.0524665646
YJR094C 0.9306357 0.0693642678
YJR152W 0.9874144 0.0125855754
YKL182W 0.8480562 0.1519438317
YKL216W 0.7426726 0.2573274172
YKR039W 0.9598101 0.0401898908
YLR081W 0.8637743 0.1362257177
YLR142W 0.6311050 0.3688949895
YLR263W 0.9977379 0.0022621377
YLR329W 0.9384954 0.0615046044
YLR420W 0.7509693 0.2490306652
YLR438W 0.9844577 0.0155423312
YML051W 0.9130079 0.0869921373
YML054C 0.9696282 0.0303717612
YML075C 0.7478846 0.2521154258
YML123C 0.9843441 0.0156559435
YMR108W 0.8708165 0.1291834951
YMR133W 0.9638260 0.0361740331
YNL052W 0.8762325 0.1237674916
YNL104C 0.8649511 0.1350488843
YNL142W 0.9609159 0.0390840768
YNL210W 0.9799331 0.0200669264
YNR001C 0.9071657 0.0928342637
YNR050C 0.9935550 0.0064449572
YOL006C 0.9048389 0.0951610717
YOR065W 0.8415163 0.1584837412
YOR120W 0.9848475 0.0151525419
YOR153W 0.5878265 0.4121734500
YOR328W 0.9327339 0.0672660511
YOR351C 0.9487537 0.0512462673
YOR375C 0.6884162 0.3115838404
YPL111W 0.8423637 0.1576362967
YPL231W 0.9782176 0.0217824326
YPR065W 0.9628781 0.0371219238
YPR138C 0.9858760 0.0141240000
YPR145W 0.7177047 0.2822953072

$permut.pc.stepwise.lda$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 CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL PHO PHO CTL
[20] CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[39] CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[58] CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL PHO CTL CTL
[77] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
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  80   8
   PHO   0   0
attr(,"error")
[1] 0.0909091



$stepwise.qda
$stepwise.qda$max.p
[1] 5

$stepwise.qda$errors
[1] 0.02272727 0.01136364 0.02272727 0.01136364 0.02272727

$stepwise.qda$confusion.table
  step              error added.var                      added.var.name CTL.CTL
1    1 0.0227272727272727         1 Low.Pi_vs_High.Pi_in_WT_.NBW7._exp1      80
2    2 0.0113636363636364         5                         pho80_vs_WT      80
3    3 0.0227272727272727         2 Low.Pi_vs_High.Pi_in_WT_.NBW7._exp2      79
4    4 0.0113636363636364         3   Low.Pi_vs_High.Pi_in_WT_.DBY7286.      80
5    5 0.0227272727272727         4                         PHO4c_vs_WT      79
  CTL.PHO PHO.CTL PHO.PHO
1       0       2       6
2       0       1       7
3       1       1       7
4       0       1       7
5       1       1       7

$stepwise.qda$best.pda
$stepwise.qda$best.pda$class
 [1] CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[20] CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[39] CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[58] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[77] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
Levels: CTL PHO

$stepwise.qda$best.pda$posterior
                 CTL          PHO
YAL038W 9.953280e-01 4.671986e-03
YAR071W 1.455943e-27 1.000000e+00
YBL005W 9.990996e-01 9.004210e-04
YBL030C 9.934202e-01 6.579781e-03
YBR006W 9.970985e-01 2.901546e-03
YBR018C 9.889949e-01 1.100508e-02
YBR020W 9.960534e-01 3.946639e-03
YBR093C 1.774129e-22 1.000000e+00
YBR115C 9.998654e-01 1.345509e-04
YBR184W 9.999267e-01 7.328879e-05
YBR296C 1.033694e-18 1.000000e+00
YCL018W 9.999277e-01 7.225492e-05
YDL131W 9.950684e-01 4.931572e-03
YDL182W 9.987330e-01 1.267029e-03
YDL205C 9.999980e-01 2.043957e-06
YDL210W 9.994399e-01 5.600585e-04
YDR011W 9.999117e-01 8.833739e-05
YDR044W 9.951526e-01 4.847404e-03
YDR234W 9.959036e-01 4.096438e-03
YDR285W 9.975981e-01 2.401938e-03
YDR406W 9.862481e-01 1.375189e-02
YDR481C 6.826552e-05 9.999317e-01
YEL021W 9.984071e-01 1.592936e-03
YEL039C 9.954730e-01 4.526971e-03
YER026C 9.972027e-01 2.797306e-03
YER086W 9.958964e-01 4.103625e-03
YER179W 9.975918e-01 2.408170e-03
YGL009C 9.999585e-01 4.152670e-05
YGL073W 9.997909e-01 2.091195e-04
YGL213C 9.996356e-01 3.643543e-04
YGR019W 9.992414e-01 7.585585e-04
YGR044C 9.996088e-01 3.912156e-04
YGR088W 9.521608e-01 4.783923e-02
YGR121C 9.996953e-01 3.047397e-04
YGR157W 9.984561e-01 1.543918e-03
YGR233C 9.974913e-01 2.508684e-03
YGR281W 9.835583e-01 1.644173e-02
YHL022C 9.971602e-01 2.839783e-03
YHR007C 9.984098e-01 1.590183e-03
YHR008C 9.971628e-01 2.837196e-03
YHR014W 9.653865e-01 3.461352e-02
YHR037W 9.973786e-01 2.621420e-03
YHR136C 5.305521e-21 1.000000e+00
YHR153C 9.999999e-01 7.364920e-08
YIL015W 9.981730e-01 1.826993e-03
YIL072W 9.998757e-01 1.243043e-04
YIR034C 9.883995e-01 1.160046e-02
YJL106W 9.935159e-01 6.484135e-03
YJL117W 2.153996e-03 9.978460e-01
YJL153C 9.997773e-01 2.226726e-04
YJL219W 9.998051e-01 1.948671e-04
YJR048W 9.992891e-01 7.108892e-04
YJR073C 9.978232e-01 2.176849e-03
YJR094C 9.999641e-01 3.585386e-05
YJR152W 9.995294e-01 4.706087e-04
YKL182W 9.989703e-01 1.029675e-03
YKL216W 9.990468e-01 9.532021e-04
YKR039W 9.983051e-01 1.694850e-03
YLR081W 9.851021e-01 1.489787e-02
YLR142W 7.854257e-01 2.145743e-01
YLR263W 9.999907e-01 9.269736e-06
YLR329W 9.982047e-01 1.795322e-03
YLR420W 9.999158e-01 8.417063e-05
YLR438W 9.973060e-01 2.694026e-03
YML051W 9.972690e-01 2.731001e-03
YML054C 9.957702e-01 4.229847e-03
YML075C 9.994406e-01 5.594008e-04
YML123C 3.598981e-33 1.000000e+00
YMR108W 9.999027e-01 9.733651e-05
YMR133W 9.977896e-01 2.210382e-03
YNL052W 9.999008e-01 9.921578e-05
YNL104C 9.946875e-01 5.312528e-03
YNL142W 9.999998e-01 1.534530e-07
YNL210W 9.999481e-01 5.193114e-05
YNR001C 9.411332e-01 5.886683e-02
YNR050C 9.995233e-01 4.766535e-04
YOL006C 9.998422e-01 1.577844e-04
YOR065W 9.999991e-01 8.607673e-07
YOR120W 9.998757e-01 1.242793e-04
YOR153W 9.941017e-01 5.898339e-03
YOR328W 9.998972e-01 1.028256e-04
YOR351C 1.000000e+00 7.817083e-14
YOR375C 9.998020e-01 1.980409e-04
YPL111W 9.999953e-01 4.739476e-06
YPL231W 9.979831e-01 2.016864e-03
YPR065W 9.938553e-01 6.144670e-03
YPR138C 9.999743e-01 2.574082e-05
YPR145W 9.999015e-01 9.846121e-05

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

$stepwise.qda$best.pda$training.names
 [1] "YAL038W" "YAR071W" "YBL005W" "YBL030C" "YBR006W" "YBR018C" "YBR020W"
 [8] "YBR093C" "YBR115C" "YBR184W" "YBR296C" "YCL018W" "YDL131W" "YDL182W"
[15] "YDL205C" "YDL210W" "YDR011W" "YDR044W" "YDR234W" "YDR285W" "YDR406W"
[22] "YDR481C" "YEL021W" "YEL039C" "YER026C" "YER086W" "YER179W" "YGL009C"
[29] "YGL073W" "YGL213C" "YGR019W" "YGR044C" "YGR088W" "YGR121C" "YGR157W"
[36] "YGR233C" "YGR281W" "YHL022C" "YHR007C" "YHR008C" "YHR014W" "YHR037W"
[43] "YHR136C" "YHR153C" "YIL015W" "YIL072W" "YIR034C" "YJL106W" "YJL117W"
[50] "YJL153C" "YJL219W" "YJR048W" "YJR073C" "YJR094C" "YJR152W" "YKL182W"
[57] "YKL216W" "YKR039W" "YLR081W" "YLR142W" "YLR263W" "YLR329W" "YLR420W"
[64] "YLR438W" "YML051W" "YML054C" "YML075C" "YML123C" "YMR108W" "YMR133W"
[71] "YNL052W" "YNL104C" "YNL142W" "YNL210W" "YNR001C" "YNR050C" "YOL006C"
[78] "YOR065W" "YOR120W" "YOR153W" "YOR328W" "YOR351C" "YOR375C" "YPL111W"
[85] "YPL231W" "YPR065W" "YPR138C" "YPR145W"

$stepwise.qda$best.pda$training.label
 [1] CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[20] CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL
[39] CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[58] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[77] CTL CTL CTL CTL CTL CTL 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  80   1
   PHO   0   7
attr(,"error")
[1] 0.01136364


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

$stepwise.qda$best.vars
[1] 1 5 2 3

$stepwise.qda$best.var.names
[1] "Low.Pi_vs_High.Pi_in_WT_.NBW7._exp1" "pho80_vs_WT"                        
[3] "Low.Pi_vs_High.Pi_in_WT_.NBW7._exp2" "Low.Pi_vs_High.Pi_in_WT_.DBY7286."  

$stepwise.qda$best.error
[1] 0.01136364

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

$stepwise.qda$var.order
[1] 1 5 2 3 4 6 7 8


$pc.stepwise.qda
$pc.stepwise.qda$max.p
[1] 5

$pc.stepwise.qda$errors
[1] 0.01136364 0.02272727 0.03409091 0.01136364 0.02272727

$pc.stepwise.qda$confusion.table
  step              error added.var added.var.name CTL.CTL CTL.PHO PHO.CTL
1    1 0.0113636363636364         1         Comp.1      80       0       1
2    2 0.0227272727272727         2         Comp.2      79       1       1
3    3 0.0340909090909091         3         Comp.3      78       2       1
4    4 0.0113636363636364         4         Comp.4      80       0       1
5    5 0.0227272727272727         5         Comp.5      79       1       1
  PHO.PHO
1       7
2       7
3       7
4       7
5       7

$pc.stepwise.qda$best.pda
$pc.stepwise.qda$best.pda$class
 [1] CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[20] CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[39] CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[58] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[77] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
Levels: CTL PHO

$pc.stepwise.qda$best.pda$posterior
                 CTL          PHO
YAL038W 9.959721e-01 4.027906e-03
YAR071W 1.902764e-56 1.000000e+00
YBL005W 9.993977e-01 6.023146e-04
YBL030C 9.907969e-01 9.203130e-03
YBR006W 9.982677e-01 1.732331e-03
YBR018C 9.970736e-01 2.926415e-03
YBR020W 9.985924e-01 1.407637e-03
YBR093C 3.350220e-39 1.000000e+00
YBR115C 9.985953e-01 1.404708e-03
YBR184W 9.998987e-01 1.013210e-04
YBR296C 7.117242e-50 1.000000e+00
YCL018W 9.999345e-01 6.553948e-05
YDL131W 9.962011e-01 3.798876e-03
YDL182W 9.983960e-01 1.604019e-03
YDL205C 9.850367e-01 1.496327e-02
YDL210W 9.996879e-01 3.120753e-04
YDR011W 9.996782e-01 3.218292e-04
YDR044W 9.841709e-01 1.582915e-02
YDR234W 9.981044e-01 1.895594e-03
YDR285W 9.896108e-01 1.038922e-02
YDR406W 9.937014e-01 6.298574e-03
YDR481C 6.079457e-09 1.000000e+00
YEL021W 9.991683e-01 8.316915e-04
YEL039C 9.983354e-01 1.664587e-03
YER026C 9.987910e-01 1.208965e-03
YER086W 9.980694e-01 1.930559e-03
YER179W 9.984759e-01 1.524123e-03
YGL009C 9.999425e-01 5.749021e-05
YGL073W 9.998860e-01 1.139942e-04
YGL213C 9.999535e-01 4.651452e-05
YGR019W 9.994394e-01 5.605636e-04
YGR044C 9.997805e-01 2.194803e-04
YGR088W 9.734322e-01 2.656783e-02
YGR121C 9.993574e-01 6.425745e-04
YGR157W 9.989785e-01 1.021541e-03
YGR233C 9.995658e-01 4.341750e-04
YGR281W 9.965435e-01 3.456549e-03
YHL022C 9.991493e-01 8.506518e-04
YHR007C 9.987667e-01 1.233336e-03
YHR008C 9.984907e-01 1.509299e-03
YHR014W 9.932101e-01 6.789885e-03
YHR037W 9.957509e-01 4.249112e-03
YHR136C 3.282899e-53 1.000000e+00
YHR153C 9.999999e-01 1.171474e-07
YIL015W 9.987401e-01 1.259938e-03
YIL072W 9.994399e-01 5.601059e-04
YIR034C 8.405395e-01 1.594605e-01
YJL106W 9.992594e-01 7.405665e-04
YJL117W 4.104498e-05 9.999590e-01
YJL153C 9.998174e-01 1.825779e-04
YJL219W 9.996087e-01 3.913382e-04
YJR048W 9.999959e-01 4.121884e-06
YJR073C 9.983557e-01 1.644344e-03
YJR094C 9.999916e-01 8.381220e-06
YJR152W 9.997273e-01 2.727020e-04
YKL182W 9.962466e-01 3.753389e-03
YKL216W 9.991199e-01 8.800998e-04
YKR039W 9.987385e-01 1.261517e-03
YLR081W 9.809075e-01 1.909254e-02
YLR142W 8.477080e-01 1.522920e-01
YLR263W 9.988231e-01 1.176851e-03
YLR329W 9.990040e-01 9.959591e-04
YLR420W 9.999377e-01 6.225768e-05
YLR438W 9.988347e-01 1.165256e-03
YML051W 9.990153e-01 9.847245e-04
YML054C 9.982105e-01 1.789488e-03
YML075C 9.996956e-01 3.043913e-04
YML123C 1.177992e-68 1.000000e+00
YMR108W 9.999809e-01 1.913218e-05
YMR133W 9.978079e-01 2.192100e-03
YNL052W 9.999980e-01 1.966092e-06
YNL104C 9.988111e-01 1.188925e-03
YNL142W 9.999998e-01 1.723927e-07
YNL210W 9.999592e-01 4.084440e-05
YNR001C 9.642812e-01 3.571884e-02
YNR050C 9.975105e-01 2.489532e-03
YOL006C 9.998250e-01 1.749544e-04
YOR065W 1.000000e+00 2.461744e-08
YOR120W 9.999550e-01 4.496506e-05
YOR153W 9.987841e-01 1.215900e-03
YOR328W 9.997687e-01 2.312977e-04
YOR351C 1.000000e+00 1.861108e-14
YOR375C 9.999896e-01 1.035945e-05
YPL111W 9.999994e-01 5.718971e-07
YPL231W 9.979873e-01 2.012650e-03
YPR065W 9.968685e-01 3.131518e-03
YPR138C 9.998722e-01 1.278344e-04
YPR145W 9.999905e-01 9.545299e-06

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

$pc.stepwise.qda$best.pda$training.names
 [1] "YAL038W" "YAR071W" "YBL005W" "YBL030C" "YBR006W" "YBR018C" "YBR020W"
 [8] "YBR093C" "YBR115C" "YBR184W" "YBR296C" "YCL018W" "YDL131W" "YDL182W"
[15] "YDL205C" "YDL210W" "YDR011W" "YDR044W" "YDR234W" "YDR285W" "YDR406W"
[22] "YDR481C" "YEL021W" "YEL039C" "YER026C" "YER086W" "YER179W" "YGL009C"
[29] "YGL073W" "YGL213C" "YGR019W" "YGR044C" "YGR088W" "YGR121C" "YGR157W"
[36] "YGR233C" "YGR281W" "YHL022C" "YHR007C" "YHR008C" "YHR014W" "YHR037W"
[43] "YHR136C" "YHR153C" "YIL015W" "YIL072W" "YIR034C" "YJL106W" "YJL117W"
[50] "YJL153C" "YJL219W" "YJR048W" "YJR073C" "YJR094C" "YJR152W" "YKL182W"
[57] "YKL216W" "YKR039W" "YLR081W" "YLR142W" "YLR263W" "YLR329W" "YLR420W"
[64] "YLR438W" "YML051W" "YML054C" "YML075C" "YML123C" "YMR108W" "YMR133W"
[71] "YNL052W" "YNL104C" "YNL142W" "YNL210W" "YNR001C" "YNR050C" "YOL006C"
[78] "YOR065W" "YOR120W" "YOR153W" "YOR328W" "YOR351C" "YOR375C" "YPL111W"
[85] "YPL231W" "YPR065W" "YPR138C" "YPR145W"

$pc.stepwise.qda$best.pda$training.label
 [1] CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[20] CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL
[39] CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[58] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[77] CTL CTL CTL CTL CTL CTL 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  80   1
   PHO   0   7
attr(,"error")
[1] 0.01136364


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

$pc.stepwise.qda$best.vars
[1] 1 2 3 4

$pc.stepwise.qda$best.var.names
[1] "Comp.1" "Comp.2" "Comp.3" "Comp.4"

$pc.stepwise.qda$best.error
[1] 0.01136364

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

$pc.stepwise.qda$var.order
[1] 1 2 3 4 5 6 7 8


$permut.stepwise.qda
$permut.stepwise.qda$errors
   permut.1  permut.2  permut.3  permut.4  permut.5  permut.6  permut.7
1 0.0909091 0.1250000 0.0909091 0.0909091 0.0909091 0.1363636 0.1363636
2 0.0909091 0.1363636 0.0909091 0.0909091 0.0909091 0.1022727 0.1136364
3 0.0909091 0.1590909 0.1022727 0.0909091 0.0909091 0.0909091 0.1022727
4 0.1818182 0.1363636 0.1363636 0.1022727 0.1590909 0.0909091 0.1022727
5 0.2159091 0.1250000 0.1363636 0.1590909 0.1590909 0.1022727 0.1022727
6        NA        NA        NA        NA        NA        NA        NA
7        NA        NA        NA        NA        NA        NA        NA
8        NA        NA        NA        NA        NA        NA        NA
   permut.8  permut.9 permut.10  err.mean     err.sd   err.sterr
1 0.1022727 0.0909091 0.0909091 0.1045455 0.01989989 0.006292897
2 0.1136364 0.0909091 0.0909091 0.1011364 0.01557182 0.004924242
3 0.1136364 0.2500000 0.1022727 0.1193182 0.05032322 0.015913600
4 0.1250000 0.1818182 0.1136364 0.1329545 0.03260657 0.010311104
5 0.1363636 0.2272727 0.1250000 0.1488636 0.04300535 0.013599487
6        NA        NA        NA       NaN         NA          NA
7        NA        NA        NA       NaN         NA          NA
8        NA        NA        NA       NaN         NA          NA

$permut.stepwise.qda$best.p
[1] 2

$permut.stepwise.qda$best.error
[1] 0.0909091

$permut.stepwise.qda$best.pda
$permut.stepwise.qda$best.pda$class
 [1] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[20] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[39] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[58] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[77] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
Levels: CTL PHO

$permut.stepwise.qda$best.pda$posterior
              CTL          PHO
YAL038W 0.8038983 1.961017e-01
YAR071W 1.0000000 3.157111e-09
YBL005W 0.7723577 2.276423e-01
YBL030C 0.9025593 9.744073e-02
YBR006W 0.7787805 2.212195e-01
YBR018C 0.7650980 2.349020e-01
YBR020W 0.7769656 2.230344e-01
YBR093C 0.6689163 3.310837e-01
YBR115C 0.8791330 1.208670e-01
YBR184W 0.7880151 2.119849e-01
YBR296C 1.0000000 8.498635e-09
YCL018W 0.8913579 1.086421e-01
YDL131W 0.8644689 1.355311e-01
YDL182W 0.8241625 1.758375e-01
YDL205C 1.0000000 2.490868e-11
YDL210W 0.7563631 2.436369e-01
YDR011W 0.9919042 8.095762e-03
YDR044W 0.9107118 8.928820e-02
YDR234W 0.9511576 4.884239e-02
YDR285W 0.9913810 8.618988e-03
YDR406W 0.9497797 5.022029e-02
YDR481C 0.9997745 2.254637e-04
YEL021W 0.9269392 7.306078e-02
YEL039C 0.7763887 2.236113e-01
YER026C 0.7979990 2.020010e-01
YER086W 0.9250619 7.493811e-02
YER179W 0.7636259 2.363741e-01
YGL009C 0.9342806 6.571941e-02
YGL073W 0.7618951 2.381049e-01
YGL213C 0.7797156 2.202844e-01
YGR019W 0.9997733 2.266609e-04
YGR044C 0.8380786 1.619214e-01
YGR088W 0.9733772 2.662283e-02
YGR121C 0.8166113 1.833887e-01
YGR157W 0.7742928 2.257072e-01
YGR233C 0.9675494 3.245058e-02
YGR281W 0.9862441 1.375593e-02
YHL022C 0.7348661 2.651339e-01
YHR007C 0.8875440 1.124560e-01
YHR008C 0.7736838 2.263162e-01
YHR014W 0.8507991 1.492009e-01
YHR037W 0.8880152 1.119848e-01
YHR136C 1.0000000 2.033464e-25
YHR153C 0.9419544 5.804564e-02
YIL015W 0.7629993 2.370007e-01
YIL072W 0.8160892 1.839108e-01
YIR034C 0.7677177 2.322823e-01
YJL106W 0.8852089 1.147911e-01
YJL117W 0.9303507 6.964933e-02
YJL153C 0.8024120 1.975880e-01
YJL219W 0.7657994 2.342006e-01
YJR048W 0.7598759 2.401241e-01
YJR073C 0.9685636 3.143638e-02
YJR094C 0.7460483 2.539517e-01
YJR152W 0.9471677 5.283228e-02
YKL182W 0.8866459 1.133541e-01
YKL216W 0.8445076 1.554924e-01
YKR039W 0.8243875 1.756125e-01
YLR081W 1.0000000 7.678268e-11
YLR142W 1.0000000 2.719615e-16
YLR263W 0.7559911 2.440089e-01
YLR329W 0.9316884 6.831156e-02
YLR420W 0.7956928 2.043072e-01
YLR438W 0.7569817 2.430183e-01
YML051W 0.8133943 1.866057e-01
YML054C 0.9508421 4.915787e-02
YML075C 0.9995554 4.446133e-04
YML123C 1.0000000 3.513929e-45
YMR108W 0.8115126 1.884874e-01
YMR133W 0.8055488 1.944512e-01
YNL052W 0.7695147 2.304853e-01
YNL104C 0.7685928 2.314072e-01
YNL142W 0.7506993 2.493007e-01
YNL210W 0.7547046 2.452954e-01
YNR001C 0.7709012 2.290988e-01
YNR050C 0.7796718 2.203282e-01
YOL006C 0.7615762 2.384238e-01
YOR065W 0.8980260 1.019740e-01
YOR120W 0.8583043 1.416957e-01
YOR153W 0.9993262 6.738013e-04
YOR328W 0.9988387 1.161263e-03
YOR351C 0.9646941 3.530592e-02
YOR375C 0.7622055 2.377945e-01
YPL111W 0.7658759 2.341241e-01
YPL231W 0.8623666 1.376334e-01
YPR065W 0.7633400 2.366600e-01
YPR138C 0.7837646 2.162354e-01
YPR145W 0.7964595 2.035405e-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 CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[20] CTL CTL PHO CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[39] PHO CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL
[58] PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[77] CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL PHO CTL
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  80   8
   PHO   0   0
attr(,"error")
[1] 0.0909091



$permut.pc.stepwise.qda
$permut.pc.stepwise.qda$errors
   permut.1  permut.2  permut.3  permut.4  permut.5  permut.6  permut.7
1 0.0909091 0.1022727 0.0909091 0.0909091 0.1363636 0.0909091 0.0909091
2 0.1250000 0.0909091 0.0909091 0.0909091 0.1363636 0.0909091 0.1818182
3 0.1477273 0.0909091 0.1818182 0.1250000 0.1250000 0.1022727 0.2272727
4 0.1363636 0.1022727 0.2045455 0.1477273 0.1363636 0.1022727 0.1818182
5 0.1250000 0.1136364 0.2386364 0.1818182 0.1363636 0.1136364 0.1931818
6        NA        NA        NA        NA        NA        NA        NA
7        NA        NA        NA        NA        NA        NA        NA
8        NA        NA        NA        NA        NA        NA        NA
   permut.8  permut.9 permut.10  err.mean     err.sd   err.sterr
1 0.0909091 0.0909091 0.1363636 0.1011364 0.01890148 0.005977172
2 0.0909091 0.1022727 0.1136364 0.1113636 0.02972942 0.009401268
3 0.1477273 0.1818182 0.1136364 0.1443182 0.04219704 0.013343875
4 0.2159091 0.2159091 0.1136364 0.1556818 0.04547033 0.014378979
5 0.1818182 0.2386364 0.1136364 0.1636364 0.05002295 0.015818646
6        NA        NA        NA       NaN         NA          NA
7        NA        NA        NA       NaN         NA          NA
8        NA        NA        NA       NaN         NA          NA

$permut.pc.stepwise.qda$best.p
[1] 5

$permut.pc.stepwise.qda$best.error
[1] 0.1136364

$permut.pc.stepwise.qda$best.pda
$permut.pc.stepwise.qda$best.pda$class
 [1] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[20] PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[39] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[58] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[77] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
Levels: CTL PHO

$permut.pc.stepwise.qda$best.pda$posterior
                 CTL           PHO
YAL038W 9.999983e-01  1.746363e-06
YAR071W 1.000000e+00 1.430877e-181
YBL005W 8.314393e-01  1.685607e-01
YBL030C 9.953158e-01  4.684222e-03
YBR006W 9.915777e-01  8.422309e-03
YBR018C 1.000000e+00  1.517037e-49
YBR020W 5.662141e-01  4.337859e-01
YBR093C 7.379703e-01  2.620297e-01
YBR115C 9.847903e-01  1.520969e-02
YBR184W 9.012002e-01  9.879985e-02
YBR296C 1.000000e+00  1.448711e-08
YCL018W 8.959977e-01  1.040023e-01
YDL131W 9.992870e-01  7.130063e-04
YDL182W 1.000000e+00  4.983065e-09
YDL205C 1.000000e+00  2.770196e-08
YDL210W 8.247813e-01  1.752187e-01
YDR011W 9.417099e-01  5.829013e-02
YDR044W 1.000000e+00  1.332083e-15
YDR234W 9.837831e-01  1.621693e-02
YDR285W 2.939639e-01  7.060361e-01
YDR406W 1.000000e+00  1.180754e-10
YDR481C 5.306600e-01  4.693400e-01
YEL021W 7.983859e-01  2.016141e-01
YEL039C 9.999983e-01  1.691196e-06
YER026C 9.996449e-01  3.551360e-04
YER086W 9.106046e-01  8.939540e-02
YER179W 9.137558e-01  8.624421e-02
YGL009C 9.295279e-01  7.047211e-02
YGL073W 9.376543e-01  6.234567e-02
YGL213C 9.067523e-01  9.324768e-02
YGR019W 9.812536e-01  1.874640e-02
YGR044C 8.755820e-01  1.244180e-01
YGR088W 1.000000e+00 1.237220e-206
YGR121C 7.163663e-01  2.836337e-01
YGR157W 9.840980e-01  1.590202e-02
YGR233C 9.999483e-01  5.167396e-05
YGR281W 9.999806e-01  1.936970e-05
YHL022C 9.999999e-01  1.114001e-07
YHR007C 9.652946e-01  3.470537e-02
YHR008C 9.997367e-01  2.633327e-04
YHR014W 8.193063e-01  1.806937e-01
YHR037W 7.873681e-01  2.126319e-01
YHR136C 9.999978e-01  2.230286e-06
YHR153C 9.999979e-01  2.076993e-06
YIL015W 9.999839e-01  1.606945e-05
YIL072W 9.654183e-01  3.458171e-02
YIR034C 8.407826e-01  1.592174e-01
YJL106W 9.984518e-01  1.548241e-03
YJL117W 8.219609e-01  1.780391e-01
YJL153C 9.592359e-01  4.076407e-02
YJL219W 8.140753e-01  1.859247e-01
YJR048W 9.611949e-01  3.880506e-02
YJR073C 1.000000e+00  4.759407e-10
YJR094C 9.584528e-01  4.154717e-02
YJR152W 1.000000e+00  4.312840e-19
YKL182W 9.999922e-01  7.843258e-06
YKL216W 9.493679e-01  5.063211e-02
YKR039W 9.722810e-01  2.771900e-02
YLR081W 9.818581e-01  1.814186e-02
YLR142W 9.756408e-01  2.435919e-02
YLR263W 1.000000e+00  1.372120e-09
YLR329W 9.910494e-01  8.950556e-03
YLR420W 9.821049e-01  1.789513e-02
YLR438W 9.963736e-01  3.626440e-03
YML051W 9.745888e-01  2.541116e-02
YML054C 9.851600e-01  1.483998e-02
YML075C 9.999933e-01  6.738352e-06
YML123C 3.427729e-07  9.999997e-01
YMR108W 6.485093e-01  3.514907e-01
YMR133W 9.974469e-01  2.553069e-03
YNL052W 9.990204e-01  9.795706e-04
YNL104C 9.254555e-01  7.454454e-02
YNL142W 1.000000e+00  3.709866e-10
YNL210W 9.937860e-01  6.213992e-03
YNR001C 8.524237e-01  1.475763e-01
YNR050C 9.604058e-01  3.959421e-02
YOL006C 8.130759e-01  1.869241e-01
YOR065W 1.000000e+00  1.948641e-08
YOR120W 9.999521e-01  4.787892e-05
YOR153W 9.999635e-01  3.646768e-05
YOR328W 9.676922e-01  3.230779e-02
YOR351C 1.000000e+00  2.206252e-29
YOR375C 8.328675e-01  1.671325e-01
YPL111W 9.999944e-01  5.630209e-06
YPL231W 1.000000e+00  1.452347e-16
YPR065W 9.999983e-01  1.680312e-06
YPR138C 9.987979e-01  1.202121e-03
YPR145W 8.922772e-01  1.077228e-01

$permut.pc.stepwise.qda$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 CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[20] CTL CTL CTL CTL CTL CTL CTL CTL PHO PHO CTL CTL CTL PHO CTL CTL CTL CTL PHO
[39] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[58] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[77] CTL CTL CTL CTL PHO CTL CTL CTL PHO CTL CTL CTL
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  78   8
   PHO   2   0
attr(,"error")
[1] 0.1136364



$max.p
[1] 8

$errors
  stepwise.lda pc.stepwise.lda permut.stepwise.lda permut.pc.stepwise.lda
1   0.02272727      0.02272727          0.09090909             0.09090909
2   0.01136364      0.02272727          0.09090909             0.09090909
3   0.01136364      0.02272727          0.09090909             0.09090909
4   0.02272727      0.02272727          0.09318182             0.09090909
5   0.02272727      0.02272727          0.09545455             0.09090909
6   0.02272727      0.02272727          0.09431818             0.09204545
7   0.02272727      0.02272727          0.10113636             0.09431818
8   0.02272727      0.02272727          0.10909091             0.09886364
  stepwise.qda pc.stepwise.qda permut.stepwise.qda permut.pc.stepwise.qda
1   0.02272727      0.01136364           0.1045455              0.1011364
2   0.01136364      0.02272727           0.1011364              0.1113636
3   0.02272727      0.03409091           0.1193182              0.1443182
4   0.01136364      0.01136364           0.1329545              0.1556818
5   0.02272727      0.02272727           0.1488636              0.1636364
6           NA              NA                 NaN                    NaN
7           NA              NA                 NaN                    NaN
8           NA              NA                 NaN                    NaN

$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           3 0.01136364      80       0       1       7
pc.stepwise.lda        8 0.02272727      80       0       2       6
permut.stepwise.lda    6 0.09090909      80       0       8       0
permut.pc.stepwise.lda 8 0.09090909      80       0       8       0
stepwise.qda           4 0.01136364      80       0       1       7
pc.stepwise.qda        4 0.01136364      80       0       1       7
permut.stepwise.qda    2 0.09090909      80       0       8       0
permut.pc.stepwise.qda 5 0.11363636      78       2       8       0

$best.errors
[1] 0.01136364

$best.vars
[1] 1 5 2

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

$best.pda
$best.pda$max.p
[1] 8

$best.pda$errors
[1] 0.02272727 0.01136364 0.01136364 0.02272727 0.02272727 0.02272727 0.02272727
[8] 0.02272727

$best.pda$confusion.table
  step              error added.var                      added.var.name CTL.CTL
1    1 0.0227272727272727         1 Low.Pi_vs_High.Pi_in_WT_.NBW7._exp1      80
2    2 0.0113636363636364         5                         pho80_vs_WT      80
3    3 0.0113636363636364         2 Low.Pi_vs_High.Pi_in_WT_.NBW7._exp2      80
4    4 0.0227272727272727         3   Low.Pi_vs_High.Pi_in_WT_.DBY7286.      80
5    5 0.0227272727272727         4                         PHO4c_vs_WT      80
6    6 0.0227272727272727         6                         pho85_vs_WT      80
7    7 0.0227272727272727         7                   PHO81c_vs_WT_exp1      80
8    8 0.0227272727272727         8                   PHO81c_vs_WT_exp2      80
  CTL.PHO PHO.CTL PHO.PHO
1       0       2       6
2       0       1       7
3       0       1       7
4       0       2       6
5       0       2       6
6       0       2       6
7       0       2       6
8       0       2       6

$best.pda$best.pda
$best.pda$best.pda$class
 [1] CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[20] CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[39] CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[58] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[77] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
Levels: CTL PHO

$best.pda$best.pda$posterior
                 CTL          PHO
YAL038W 9.999903e-01 9.699651e-06
YAR071W 8.314360e-13 1.000000e+00
YBL005W 9.999988e-01 1.181800e-06
YBL030C 9.999887e-01 1.127009e-05
YBR006W 9.999997e-01 3.077050e-07
YBR018C 1.000000e+00 4.844014e-09
YBR020W 1.000000e+00 7.091282e-09
YBR093C 1.248449e-08 1.000000e+00
YBR115C 9.999718e-01 2.816701e-05
YBR184W 9.999997e-01 3.072343e-07
YBR296C 4.281576e-05 9.999572e-01
YCL018W 9.999989e-01 1.084210e-06
YDL131W 9.999899e-01 1.006793e-05
YDL182W 9.999998e-01 1.846237e-07
YDL205C 9.999604e-01 3.957552e-05
YDL210W 1.000000e+00 2.831793e-09
YDR011W 9.999995e-01 4.960685e-07
YDR044W 9.999813e-01 1.874503e-05
YDR234W 9.999997e-01 3.254264e-07
YDR285W 1.000000e+00 6.258363e-09
YDR406W 9.999473e-01 5.268268e-05
YDR481C 2.200900e-01 7.799100e-01
YEL021W 9.999997e-01 2.994953e-07
YEL039C 9.999982e-01 1.786563e-06
YER026C 9.999998e-01 2.419350e-07
YER086W 9.999877e-01 1.228879e-05
YER179W 1.000000e+00 3.674796e-08
YGL009C 9.999999e-01 1.487919e-07
YGL073W 9.999998e-01 1.843317e-07
YGL213C 9.999993e-01 7.444542e-07
YGR019W 9.999994e-01 6.056626e-07
YGR044C 9.999991e-01 9.301657e-07
YGR088W 9.999994e-01 6.416167e-07
YGR121C 9.999996e-01 3.574032e-07
YGR157W 9.999991e-01 9.005669e-07
YGR233C 9.999999e-01 6.031587e-08
YGR281W 9.999509e-01 4.905170e-05
YHL022C 1.000000e+00 1.180719e-12
YHR007C 1.000000e+00 5.628900e-09
YHR008C 9.999977e-01 2.290222e-06
YHR014W 1.000000e+00 2.284793e-13
YHR037W 1.000000e+00 2.510164e-09
YHR136C 2.677966e-04 9.997322e-01
YHR153C 1.000000e+00 2.458479e-08
YIL015W 1.000000e+00 3.852989e-09
YIL072W 9.999990e-01 1.030372e-06
YIR034C 9.999301e-01 6.988400e-05
YJL106W 9.999999e-01 6.792651e-08
YJL117W 2.213877e-01 7.786123e-01
YJL153C 9.999948e-01 5.216890e-06
YJL219W 1.000000e+00 4.573466e-08
YJR048W 9.999991e-01 8.776323e-07
YJR073C 1.000000e+00 1.390449e-08
YJR094C 1.000000e+00 3.437138e-09
YJR152W 9.999999e-01 1.252817e-07
YKL182W 9.999990e-01 9.696311e-07
YKL216W 9.999995e-01 5.476115e-07
YKR039W 9.999999e-01 8.159330e-08
YLR081W 9.999830e-01 1.696514e-05
YLR142W 9.976662e-01 2.333812e-03
YLR263W 1.000000e+00 8.274063e-09
YLR329W 1.000000e+00 5.446114e-09
YLR420W 9.999989e-01 1.105357e-06
YLR438W 9.999997e-01 2.686162e-07
YML051W 9.999993e-01 7.497552e-07
YML054C 1.000000e+00 1.341231e-09
YML075C 9.999987e-01 1.295556e-06
YML123C 4.781575e-14 1.000000e+00
YMR108W 1.000000e+00 9.214187e-09
YMR133W 1.000000e+00 1.138751e-08
YNL052W 9.999979e-01 2.087206e-06
YNL104C 9.999800e-01 1.995405e-05
YNL142W 1.000000e+00 5.756135e-09
YNL210W 1.000000e+00 2.707138e-08
YNR001C 9.998591e-01 1.409030e-04
YNR050C 1.000000e+00 4.112449e-08
YOL006C 9.999996e-01 4.294339e-07
YOR065W 9.999994e-01 5.613023e-07
YOR120W 9.999999e-01 9.944845e-08
YOR153W 9.987647e-01 1.235309e-03
YOR328W 9.999993e-01 7.008550e-07
YOR351C 1.000000e+00 6.615833e-12
YOR375C 9.999990e-01 9.669330e-07
YPL111W 9.999996e-01 4.189593e-07
YPL231W 9.999989e-01 1.104782e-06
YPR065W 1.000000e+00 3.924103e-10
YPR138C 1.000000e+00 3.280658e-08
YPR145W 9.999998e-01 1.877432e-07

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

$best.pda$best.pda$training.names
 [1] "YAL038W" "YAR071W" "YBL005W" "YBL030C" "YBR006W" "YBR018C" "YBR020W"
 [8] "YBR093C" "YBR115C" "YBR184W" "YBR296C" "YCL018W" "YDL131W" "YDL182W"
[15] "YDL205C" "YDL210W" "YDR011W" "YDR044W" "YDR234W" "YDR285W" "YDR406W"
[22] "YDR481C" "YEL021W" "YEL039C" "YER026C" "YER086W" "YER179W" "YGL009C"
[29] "YGL073W" "YGL213C" "YGR019W" "YGR044C" "YGR088W" "YGR121C" "YGR157W"
[36] "YGR233C" "YGR281W" "YHL022C" "YHR007C" "YHR008C" "YHR014W" "YHR037W"
[43] "YHR136C" "YHR153C" "YIL015W" "YIL072W" "YIR034C" "YJL106W" "YJL117W"
[50] "YJL153C" "YJL219W" "YJR048W" "YJR073C" "YJR094C" "YJR152W" "YKL182W"
[57] "YKL216W" "YKR039W" "YLR081W" "YLR142W" "YLR263W" "YLR329W" "YLR420W"
[64] "YLR438W" "YML051W" "YML054C" "YML075C" "YML123C" "YMR108W" "YMR133W"
[71] "YNL052W" "YNL104C" "YNL142W" "YNL210W" "YNR001C" "YNR050C" "YOL006C"
[78] "YOR065W" "YOR120W" "YOR153W" "YOR328W" "YOR351C" "YOR375C" "YPL111W"
[85] "YPL231W" "YPR065W" "YPR138C" "YPR145W"

$best.pda$best.pda$training.label
 [1] CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[20] CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL
[39] CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[58] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL
[77] CTL CTL CTL CTL CTL CTL 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  80   1
   PHO   0   7
attr(,"error")
[1] 0.01136364


$best.pda$best.p
[1] 3

$best.pda$best.vars
[1] 1 5 2

$best.pda$best.var.names
[1] "Low.Pi_vs_High.Pi_in_WT_.NBW7._exp1" "pho80_vs_WT"                        
[3] "Low.Pi_vs_High.Pi_in_WT_.NBW7._exp2"

$best.pda$best.error
[1] 0.01136364

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

$best.pda$var.order
[1] 1 5 2 3 4 6 7 8


