$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 0.02272727

$stepwise.lda$confusion.table
  step              error added.var                      added.var.name CTL.CTL CTL.PHO PHO.CTL PHO.PHO
1    1 0.0227272727272727         1 Low.Pi_vs_High.Pi_in_WT_.NBW7._exp1      80       0       2       6
2    2 0.0113636363636364         5                         pho80_vs_WT      80       0       1       7
3    3 0.0113636363636364         2 Low.Pi_vs_High.Pi_in_WT_.NBW7._exp2      80       0       1       7
4    4 0.0227272727272727         3   Low.Pi_vs_High.Pi_in_WT_.DBY7286.      80       0       2       6
5    5 0.0227272727272727         4                         PHO4c_vs_WT      80       0       2       6
6    6 0.0227272727272727         6                         pho85_vs_WT      80       0       2       6
7    7 0.0227272727272727         7                   PHO81c_vs_WT_exp1      80       0       2       6
8    8 0.0227272727272727         8                   PHO81c_vs_WT_exp2      80       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 CTL CTL PHO CTL CTL CTL CTL CTL CTL
[29] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL
[57] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[85] 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" "YBR093C" "YBR115C" "YBR184W" "YBR296C"
[12] "YCL018W" "YDL131W" "YDL182W" "YDL205C" "YDL210W" "YDR011W" "YDR044W" "YDR234W" "YDR285W" "YDR406W" "YDR481C"
[23] "YEL021W" "YEL039C" "YER026C" "YER086W" "YER179W" "YGL009C" "YGL073W" "YGL213C" "YGR019W" "YGR044C" "YGR088W"
[34] "YGR121C" "YGR157W" "YGR233C" "YGR281W" "YHL022C" "YHR007C" "YHR008C" "YHR014W" "YHR037W" "YHR136C" "YHR153C"
[45] "YIL015W" "YIL072W" "YIR034C" "YJL106W" "YJL117W" "YJL153C" "YJL219W" "YJR048W" "YJR073C" "YJR094C" "YJR152W"
[56] "YKL182W" "YKL216W" "YKR039W" "YLR081W" "YLR142W" "YLR263W" "YLR329W" "YLR420W" "YLR438W" "YML051W" "YML054C"
[67] "YML075C" "YML123C" "YMR108W" "YMR133W" "YNL052W" "YNL104C" "YNL142W" "YNL210W" "YNR001C" "YNR050C" "YOL006C"
[78] "YOR065W" "YOR120W" "YOR153W" "YOR328W" "YOR351C" "YOR375C" "YPL111W" "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 CTL CTL PHO CTL CTL CTL CTL CTL CTL
[29] CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL
[57] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[85] 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"                         "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 0.02272727

$pc.stepwise.lda$confusion.table
  step              error added.var added.var.name CTL.CTL CTL.PHO PHO.CTL PHO.PHO
1    1 0.0227272727272727         1         Comp.1      80       0       2       6
2    2 0.0227272727272727         2         Comp.2      80       0       2       6
3    3 0.0227272727272727         3         Comp.3      80       0       2       6
4    4 0.0227272727272727         4         Comp.4      80       0       2       6
5    5 0.0227272727272727         5         Comp.5      80       0       2       6
6    6 0.0227272727272727         6         Comp.6      80       0       2       6
7    7 0.0227272727272727         7         Comp.7      80       0       2       6
8    8 0.0227272727272727         8         Comp.8      80       0       2       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 CTL CTL PHO CTL CTL CTL CTL CTL CTL
[29] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[57] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[85] 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" "YBR093C" "YBR115C" "YBR184W" "YBR296C"
[12] "YCL018W" "YDL131W" "YDL182W" "YDL205C" "YDL210W" "YDR011W" "YDR044W" "YDR234W" "YDR285W" "YDR406W" "YDR481C"
[23] "YEL021W" "YEL039C" "YER026C" "YER086W" "YER179W" "YGL009C" "YGL073W" "YGL213C" "YGR019W" "YGR044C" "YGR088W"
[34] "YGR121C" "YGR157W" "YGR233C" "YGR281W" "YHL022C" "YHR007C" "YHR008C" "YHR014W" "YHR037W" "YHR136C" "YHR153C"
[45] "YIL015W" "YIL072W" "YIR034C" "YJL106W" "YJL117W" "YJL153C" "YJL219W" "YJR048W" "YJR073C" "YJR094C" "YJR152W"
[56] "YKL182W" "YKL216W" "YKR039W" "YLR081W" "YLR142W" "YLR263W" "YLR329W" "YLR420W" "YLR438W" "YML051W" "YML054C"
[67] "YML075C" "YML123C" "YMR108W" "YMR133W" "YNL052W" "YNL104C" "YNL142W" "YNL210W" "YNR001C" "YNR050C" "YOL006C"
[78] "YOR065W" "YOR120W" "YOR153W" "YOR328W" "YOR351C" "YOR375C" "YPL111W" "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 CTL CTL PHO CTL CTL CTL CTL CTL CTL
[29] CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL
[57] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[85] 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
$permut.stepwise.lda$max.p
[1] 8

$permut.stepwise.lda$errors
[1] 0.07954545 0.07954545 0.07954545 0.07954545 0.07954545 0.09090909 0.10227273 0.10227273

$permut.stepwise.lda$confusion.table
  step              error added.var                      added.var.name CTL.CTL CTL.PHO PHO.CTL PHO.PHO
1    1 0.0795454545454546         8                   PHO81c_vs_WT_exp2      80       0       7       1
2    2 0.0795454545454546         1 Low.Pi_vs_High.Pi_in_WT_.NBW7._exp1      80       0       7       1
3    3 0.0795454545454546         3   Low.Pi_vs_High.Pi_in_WT_.DBY7286.      80       0       7       1
4    4 0.0795454545454546         2 Low.Pi_vs_High.Pi_in_WT_.NBW7._exp2      80       0       7       1
5    5 0.0795454545454546         6                         pho85_vs_WT      80       0       7       1
6    6  0.090909090909091         4                         PHO4c_vs_WT      80       0       8       0
7    7  0.102272727272727         5                         pho80_vs_WT      79       1       8       0
8    8  0.102272727272727         7                   PHO81c_vs_WT_exp1      79       1       8       0

$permut.stepwise.lda$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 CTL CTL CTL CTL CTL CTL CTL CTL CTL
[29] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[57] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[85] CTL CTL CTL CTL
Levels: CTL PHO

$permut.stepwise.lda$best.pda$posterior
              CTL          PHO
YAR003W 0.9520456 4.795438e-02
YAR064W 0.9605876 3.941239e-02
YBL021C 0.9679041 3.209594e-02
YBL047C 0.9092715 9.072848e-02
YBL090W 0.8912533 1.087467e-01
YBL113C 0.8487624 1.512376e-01
YBR042C 0.9328412 6.715878e-02
YBR275C 0.9587858 4.121424e-02
YCR060W 0.9021786 9.782139e-02
YDL052C 0.8664503 1.335497e-01
YDL100C 0.9584542 4.154579e-02
YDL243C 0.9690415 3.095849e-02
YDR024W 0.9774370 2.256301e-02
YDR151C 0.9397991 6.020085e-02
YDR230W 0.9710769 2.892312e-02
YDR265W 0.9693274 3.067256e-02
YDR288W 0.8969556 1.030444e-01
YDR318W 0.9389371 6.106294e-02
YDR341C 0.9395778 6.042220e-02
YDR392W 0.9441449 5.585506e-02
YDR399W 0.9999925 7.535932e-06
YDR429C 0.9808782 1.912176e-02
YDR526C 0.9787218 2.127820e-02
YEL064C 0.9687154 3.128456e-02
YER015W 0.9617999 3.820012e-02
YER078C 0.9532348 4.676525e-02
YER081W 0.7790737 2.209263e-01
YER136W 0.8685989 1.314011e-01
YFL039C 0.8110029 1.889971e-01
YFL053W 0.9902183 9.781694e-03
YFR046C 0.9325197 6.748031e-02
YGL132W 0.9606873 3.931275e-02
YGL143C 0.9587571 4.124287e-02
YGL148W 0.9797587 2.024130e-02
YGR134W 0.8953414 1.046586e-01
YHR079C 0.9451695 5.483055e-02
YHR133C 0.8888164 1.111836e-01
YHR211W 0.9902205 9.779491e-03
YIR042C 0.8299015 1.700985e-01
YJL012C 0.4257997 5.742003e-01
YJL034W 0.9127501 8.724993e-02
YJL051W 0.9753780 2.462200e-02
YJR064W 0.9543991 4.560092e-02
YJR098C 0.9799806 2.001940e-02
YKL076C 0.9189429 8.105712e-02
YKL098W 0.9513820 4.861802e-02
YKL108W 0.9667765 3.322350e-02
YKL128C 0.7403927 2.596073e-01
YKL152C 0.8330887 1.669113e-01
YKL196C 0.9359252 6.407481e-02
YKR027W 0.9225246 7.747542e-02
YKR072C 0.9501377 4.986229e-02
YLL029W 0.8527986 1.472014e-01
YLR032W 0.9888895 1.111053e-02
YLR056W 0.8375590 1.624410e-01
YLR123C 0.9220211 7.797890e-02
YLR143W 0.9864960 1.350399e-02
YLR250W 0.9518273 4.817266e-02
YLR327C 0.5109613 4.890387e-01
YLR332W 0.9667506 3.324944e-02
YML066C 0.9518598 4.814018e-02
YML069W 0.9176297 8.237028e-02
YML113W 0.9741340 2.586604e-02
YML120C 0.8497477 1.502523e-01
YMR059W 0.9766015 2.339850e-02
YMR091C 0.9907279 9.272150e-03
YMR092C 0.9287441 7.125591e-02
YNL008C 0.9486984 5.130155e-02
YNL031C 0.9407444 5.925564e-02
YNL039W 0.9589720 4.102797e-02
YNL056W 0.8496259 1.503741e-01
YNL120C 0.9922955 7.704451e-03
YNL243W 0.9632240 3.677598e-02
YNL247W 0.9747171 2.528293e-02
YNL285W 0.9794829 2.051713e-02
YNL308C 0.9817343 1.826567e-02
YOR023C 0.9712362 2.876385e-02
YOR248W 0.9696424 3.035756e-02
YOR278W 0.8810651 1.189349e-01
YOR296W 0.9775519 2.244808e-02
YOR298W 0.9530825 4.691746e-02
YPL022W 0.9663830 3.361696e-02
YPL032C 0.9965044 3.495622e-03
YPL136W 0.9591811 4.081886e-02
YPL182C 0.9728609 2.713912e-02
YPR099C 0.9381867 6.181333e-02
YPR156C 0.7997022 2.002978e-01
YPR157W 0.9329434 6.705664e-02

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

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

$permut.stepwise.lda$best.pda$training.label
 [1] CTL CTL PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL PHO CTL CTL
[29] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[57] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL
[85] CTL CTL CTL PHO
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   7
   PHO   0   1
attr(,"error")
[1] 0.07954545


$permut.stepwise.lda$best.p
[1] 5

$permut.stepwise.lda$best.vars
[1] 8 1 3 2 6

$permut.stepwise.lda$best.var.names
[1] "PHO81c_vs_WT_exp2"                   "Low.Pi_vs_High.Pi_in_WT_.NBW7._exp1" "Low.Pi_vs_High.Pi_in_WT_.DBY7286."  
[4] "Low.Pi_vs_High.Pi_in_WT_.NBW7._exp2" "pho85_vs_WT"                        

$permut.stepwise.lda$best.error
[1] 0.07954545

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

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


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

$permut.pc.stepwise.lda$errors
[1] 0.09090909 0.07954545 0.07954545 0.07954545 0.07954545 0.09090909 0.09090909 0.10227273

$permut.pc.stepwise.lda$confusion.table
  step              error added.var added.var.name CTL.CTL CTL.PHO PHO.CTL PHO.PHO
1    1  0.090909090909091         1         Comp.1      80       0       8       0
2    2 0.0795454545454546         6         Comp.6      80       0       7       1
3    3 0.0795454545454546         3         Comp.3      80       0       7       1
4    4 0.0795454545454546         2         Comp.2      80       0       7       1
5    5 0.0795454545454546         7         Comp.7      80       0       7       1
6    6  0.090909090909091         4         Comp.4      80       0       8       0
7    7  0.090909090909091         5         Comp.5      80       0       8       0
8    8  0.102272727272727         8         Comp.8      79       1       8       0

$permut.pc.stepwise.lda$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 CTL CTL CTL CTL CTL CTL CTL CTL CTL
[29] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[57] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[85] CTL CTL CTL CTL
Levels: CTL PHO

$permut.pc.stepwise.lda$best.pda$posterior
              CTL          PHO
YAR003W 0.9564058 4.359418e-02
YAR064W 0.9428030 5.719699e-02
YBL021C 0.9637343 3.626573e-02
YBL047C 0.8673381 1.326619e-01
YBL090W 0.9243780 7.562197e-02
YBL113C 0.7394986 2.605014e-01
YBR042C 0.8913275 1.086725e-01
YBR275C 0.9596287 4.037128e-02
YCR060W 0.9002246 9.977540e-02
YDL052C 0.8734039 1.265961e-01
YDL100C 0.9654332 3.456682e-02
YDL243C 0.6620797 3.379203e-01
YDR024W 0.9759288 2.407123e-02
YDR151C 0.9709955 2.900453e-02
YDR230W 0.9740413 2.595866e-02
YDR265W 0.9488039 5.119612e-02
YDR288W 0.8909588 1.090412e-01
YDR318W 0.9612031 3.879690e-02
YDR341C 0.9349826 6.501743e-02
YDR392W 0.9650296 3.497036e-02
YDR399W 0.9999995 5.392540e-07
YDR429C 0.9871523 1.284775e-02
YDR526C 0.9792553 2.074466e-02
YEL064C 0.9631652 3.683484e-02
YER015W 0.9633875 3.661250e-02
YER078C 0.9591059 4.089406e-02
YER081W 0.8400973 1.599027e-01
YER136W 0.8753410 1.246590e-01
YFL039C 0.8834268 1.165732e-01
YFL053W 0.9892138 1.078616e-02
YFR046C 0.9497093 5.029072e-02
YGL132W 0.9515556 4.844440e-02
YGL143C 0.9619773 3.802271e-02
YGL148W 0.9752199 2.478010e-02
YGR134W 0.9162968 8.370318e-02
YHR079C 0.9402012 5.979876e-02
YHR133C 0.9159470 8.405297e-02
YHR211W 0.9871150 1.288496e-02
YIR042C 0.8460941 1.539059e-01
YJL012C 0.4857295 5.142705e-01
YJL034W 0.9295381 7.046193e-02
YJL051W 0.9822691 1.773086e-02
YJR064W 0.9438645 5.613550e-02
YJR098C 0.9772929 2.270714e-02
YKL076C 0.9346297 6.537030e-02
YKL098W 0.9313105 6.868947e-02
YKL108W 0.9663355 3.366448e-02
YKL128C 0.8038592 1.961408e-01
YKL152C 0.8843291 1.156709e-01
YKL196C 0.9680155 3.198453e-02
YKR027W 0.9065617 9.343826e-02
YKR072C 0.8927969 1.072031e-01
YLL029W 0.9017888 9.821118e-02
YLR032W 0.9672718 3.272822e-02
YLR056W 0.8112930 1.887070e-01
YLR123C 0.9121661 8.783390e-02
YLR143W 0.9769362 2.306377e-02
YLR250W 0.9219311 7.806893e-02
YLR327C 0.7735827 2.264173e-01
YLR332W 0.9531974 4.680257e-02
YML066C 0.9338654 6.613456e-02
YML069W 0.9324262 6.757380e-02
YML113W 0.9763357 2.366430e-02
YML120C 0.9104828 8.951717e-02
YMR059W 0.9776863 2.231368e-02
YMR091C 0.9779842 2.201578e-02
YMR092C 0.9177042 8.229582e-02
YNL008C 0.9520338 4.796618e-02
YNL031C 0.9672451 3.275487e-02
YNL039W 0.9670752 3.292480e-02
YNL056W 0.9088910 9.110902e-02
YNL120C 0.9865010 1.349898e-02
YNL243W 0.9393891 6.061090e-02
YNL247W 0.9690630 3.093696e-02
YNL285W 0.9490327 5.096725e-02
YNL308C 0.9735427 2.645728e-02
YOR023C 0.9642126 3.578740e-02
YOR248W 0.9799529 2.004713e-02
YOR278W 0.9256731 7.432692e-02
YOR296W 0.9807636 1.923637e-02
YOR298W 0.9552940 4.470599e-02
YPL022W 0.9533080 4.669202e-02
YPL032C 0.9811920 1.880797e-02
YPL136W 0.9855538 1.444619e-02
YPL182C 0.9635908 3.640924e-02
YPR099C 0.9623673 3.763270e-02
YPR156C 0.8434227 1.565773e-01
YPR157W 0.9057106 9.428942e-02

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

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

$permut.pc.stepwise.lda$best.pda$training.label
 [1] CTL CTL PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL PHO CTL CTL
[29] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[57] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL
[85] 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  80   7
   PHO   0   1
attr(,"error")
[1] 0.07954545


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

$permut.pc.stepwise.lda$best.vars
[1] 1 6 3 2 7

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

$permut.pc.stepwise.lda$best.error
[1] 0.07954545

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

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


$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 CTL.PHO PHO.CTL PHO.PHO
1    1 0.0227272727272727         1 Low.Pi_vs_High.Pi_in_WT_.NBW7._exp1      80       0       2       6
2    2 0.0113636363636364         5                         pho80_vs_WT      80       0       1       7
3    3 0.0227272727272727         2 Low.Pi_vs_High.Pi_in_WT_.NBW7._exp2      79       1       1       7
4    4 0.0113636363636364         3   Low.Pi_vs_High.Pi_in_WT_.DBY7286.      80       0       1       7
5    5 0.0227272727272727         4                         PHO4c_vs_WT      79       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 CTL CTL PHO CTL CTL CTL CTL CTL CTL
[29] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL
[57] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[85] 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" "YBR093C" "YBR115C" "YBR184W" "YBR296C"
[12] "YCL018W" "YDL131W" "YDL182W" "YDL205C" "YDL210W" "YDR011W" "YDR044W" "YDR234W" "YDR285W" "YDR406W" "YDR481C"
[23] "YEL021W" "YEL039C" "YER026C" "YER086W" "YER179W" "YGL009C" "YGL073W" "YGL213C" "YGR019W" "YGR044C" "YGR088W"
[34] "YGR121C" "YGR157W" "YGR233C" "YGR281W" "YHL022C" "YHR007C" "YHR008C" "YHR014W" "YHR037W" "YHR136C" "YHR153C"
[45] "YIL015W" "YIL072W" "YIR034C" "YJL106W" "YJL117W" "YJL153C" "YJL219W" "YJR048W" "YJR073C" "YJR094C" "YJR152W"
[56] "YKL182W" "YKL216W" "YKR039W" "YLR081W" "YLR142W" "YLR263W" "YLR329W" "YLR420W" "YLR438W" "YML051W" "YML054C"
[67] "YML075C" "YML123C" "YMR108W" "YMR133W" "YNL052W" "YNL104C" "YNL142W" "YNL210W" "YNR001C" "YNR050C" "YOL006C"
[78] "YOR065W" "YOR120W" "YOR153W" "YOR328W" "YOR351C" "YOR375C" "YPL111W" "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 CTL CTL PHO CTL CTL CTL CTL CTL CTL
[29] CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL
[57] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[85] 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"                         "Low.Pi_vs_High.Pi_in_WT_.NBW7._exp2"
[4] "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 PHO.PHO
1    1 0.0113636363636364         1         Comp.1      80       0       1       7
2    2 0.0227272727272727         2         Comp.2      79       1       1       7
3    3 0.0340909090909091         3         Comp.3      78       2       1       7
4    4 0.0113636363636364         4         Comp.4      80       0       1       7
5    5 0.0227272727272727         5         Comp.5      79       1       1       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 CTL CTL PHO CTL CTL CTL CTL CTL CTL
[29] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL
[57] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[85] 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" "YBR093C" "YBR115C" "YBR184W" "YBR296C"
[12] "YCL018W" "YDL131W" "YDL182W" "YDL205C" "YDL210W" "YDR011W" "YDR044W" "YDR234W" "YDR285W" "YDR406W" "YDR481C"
[23] "YEL021W" "YEL039C" "YER026C" "YER086W" "YER179W" "YGL009C" "YGL073W" "YGL213C" "YGR019W" "YGR044C" "YGR088W"
[34] "YGR121C" "YGR157W" "YGR233C" "YGR281W" "YHL022C" "YHR007C" "YHR008C" "YHR014W" "YHR037W" "YHR136C" "YHR153C"
[45] "YIL015W" "YIL072W" "YIR034C" "YJL106W" "YJL117W" "YJL153C" "YJL219W" "YJR048W" "YJR073C" "YJR094C" "YJR152W"
[56] "YKL182W" "YKL216W" "YKR039W" "YLR081W" "YLR142W" "YLR263W" "YLR329W" "YLR420W" "YLR438W" "YML051W" "YML054C"
[67] "YML075C" "YML123C" "YMR108W" "YMR133W" "YNL052W" "YNL104C" "YNL142W" "YNL210W" "YNR001C" "YNR050C" "YOL006C"
[78] "YOR065W" "YOR120W" "YOR153W" "YOR328W" "YOR351C" "YOR375C" "YPL111W" "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 CTL CTL PHO CTL CTL CTL CTL CTL CTL
[29] CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL
[57] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[85] 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
$permut.stepwise.qda$max.p
[1] 5

$permut.stepwise.qda$errors
[1] 0.1022727 0.1022727 0.0909091 0.1250000 0.1363636

$permut.stepwise.qda$confusion.table
  step             error added.var                      added.var.name CTL.CTL CTL.PHO PHO.CTL PHO.PHO
1    1 0.102272727272727         8                   PHO81c_vs_WT_exp2      78       2       7       1
2    2 0.102272727272727         1 Low.Pi_vs_High.Pi_in_WT_.NBW7._exp1      78       2       7       1
3    3 0.090909090909091         3   Low.Pi_vs_High.Pi_in_WT_.DBY7286.      80       0       8       0
4    4             0.125         2 Low.Pi_vs_High.Pi_in_WT_.NBW7._exp2      77       3       8       0
5    5 0.136363636363636         6                         pho85_vs_WT      76       4       8       0

$permut.stepwise.qda$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 CTL CTL CTL CTL CTL CTL CTL CTL CTL
[29] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[57] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[85] CTL CTL CTL CTL
Levels: CTL PHO

$permut.stepwise.qda$best.pda$posterior
              CTL          PHO
YAR003W 0.9599531 4.004694e-02
YAR064W 0.9861142 1.388583e-02
YBL021C 0.9866396 1.336038e-02
YBL047C 0.9393135 6.068650e-02
YBL090W 0.9775331 2.246692e-02
YBL113C 0.8906781 1.093219e-01
YBR042C 0.9631834 3.681655e-02
YBR275C 0.9800157 1.998428e-02
YCR060W 0.9540233 4.597673e-02
YDL052C 0.9547164 4.528360e-02
YDL100C 0.9713588 2.864117e-02
YDL243C 0.9238107 7.618934e-02
YDR024W 0.9870632 1.293684e-02
YDR151C 0.9775498 2.245020e-02
YDR230W 0.9854542 1.454583e-02
YDR265W 0.9757224 2.427761e-02
YDR288W 0.9679159 3.208410e-02
YDR318W 0.9776584 2.234164e-02
YDR341C 0.9697523 3.024765e-02
YDR392W 0.9740328 2.596722e-02
YDR399W 0.9659514 3.404856e-02
YDR429C 0.8357618 1.642382e-01
YDR526C 0.9659487 3.405126e-02
YEL064C 0.9810532 1.894677e-02
YER015W 0.9815812 1.841883e-02
YER078C 0.9838987 1.610134e-02
YER081W 0.9349423 6.505767e-02
YER136W 0.9132447 8.675529e-02
YFL039C 0.8934644 1.065356e-01
YFL053W 0.7814495 2.185505e-01
YFR046C 0.9757305 2.426954e-02
YGL132W 0.9771224 2.287757e-02
YGL143C 0.9703424 2.965760e-02
YGL148W 0.8414254 1.585746e-01
YGR134W 0.9678602 3.213982e-02
YHR079C 0.9732596 2.674041e-02
YHR133C 0.9668990 3.310105e-02
YHR211W 0.9746406 2.535944e-02
YIR042C 0.9571739 4.282608e-02
YJL012C 0.9295163 7.048371e-02
YJL034W 0.9785071 2.149292e-02
YJL051W 0.9756335 2.436647e-02
YJR064W 0.9698085 3.019154e-02
YJR098C 0.9765704 2.342958e-02
YKL076C 0.9746619 2.533809e-02
YKL098W 0.9714438 2.855616e-02
YKL108W 0.9747674 2.523262e-02
YKL128C 0.7813706 2.186294e-01
YKL152C 0.9455558 5.444415e-02
YKL196C 0.9763204 2.367956e-02
YKR027W 0.9708243 2.917567e-02
YKR072C 0.9324229 6.757708e-02
YLL029W 0.9444649 5.553507e-02
YLR032W 0.9814088 1.859117e-02
YLR056W 0.7311375 2.688625e-01
YLR123C 0.9846771 1.532289e-02
YLR143W 0.8621947 1.378053e-01
YLR250W 0.9829051 1.709486e-02
YLR327C 0.9926933 7.306677e-03
YLR332W 0.9867787 1.322133e-02
YML066C 0.9710717 2.892825e-02
YML069W 0.9720064 2.799364e-02
YML113W 0.9545704 4.542963e-02
YML120C 0.8398614 1.601386e-01
YMR059W 0.9663155 3.368449e-02
YMR091C 0.9546810 4.531896e-02
YMR092C 0.9713389 2.866111e-02
YNL008C 0.9830150 1.698497e-02
YNL031C 0.9700451 2.995486e-02
YNL039W 0.9765878 2.341222e-02
YNL056W 0.9540987 4.590129e-02
YNL120C 0.8010509 1.989491e-01
YNL243W 0.9776436 2.235636e-02
YNL247W 0.9698079 3.019209e-02
YNL285W 0.9726032 2.739675e-02
YNL308C 0.9802806 1.971938e-02
YOR023C 0.9829159 1.708413e-02
YOR248W 0.9787921 2.120795e-02
YOR278W 0.7471624 2.528376e-01
YOR296W 0.9459765 5.402346e-02
YOR298W 0.9757598 2.424022e-02
YPL022W 0.9821978 1.780219e-02
YPL032C 0.9996859 3.140791e-04
YPL136W 0.9514182 4.858176e-02
YPL182C 0.9751886 2.481142e-02
YPR099C 0.9734298 2.657017e-02
YPR156C 0.7693486 2.306514e-01
YPR157W 1.0000000 6.080785e-10

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

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

$permut.stepwise.qda$best.pda$training.label
 [1] CTL CTL PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL PHO CTL CTL
[29] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[57] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL
[85] CTL CTL 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  80   8
   PHO   0   0
attr(,"error")
[1] 0.0909091


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

$permut.stepwise.qda$best.vars
[1] 8 1 3

$permut.stepwise.qda$best.var.names
[1] "PHO81c_vs_WT_exp2"                   "Low.Pi_vs_High.Pi_in_WT_.NBW7._exp1" "Low.Pi_vs_High.Pi_in_WT_.DBY7286."  

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

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

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


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

$permut.pc.stepwise.qda$errors
[1] 0.0909091 0.1250000 0.1136364 0.1022727 0.1022727

$permut.pc.stepwise.qda$confusion.table
  step             error added.var added.var.name CTL.CTL CTL.PHO PHO.CTL PHO.PHO
1    1 0.090909090909091         1         Comp.1      79       1       7       1
2    2             0.125         6         Comp.6      77       3       8       0
3    3 0.113636363636364         3         Comp.3      78       2       8       0
4    4 0.102272727272727         2         Comp.2      79       1       8       0
5    5 0.102272727272727         7         Comp.7      79       1       8       0

$permut.pc.stepwise.qda$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 CTL CTL CTL CTL CTL CTL CTL CTL CTL
[29] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[57] CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[85] CTL CTL CTL CTL
Levels: CTL PHO

$permut.pc.stepwise.qda$best.pda$posterior
               CTL        PHO
 [1,] 9.782956e-01 0.02170436
 [2,] 9.725135e-01 0.02748650
 [3,] 9.752679e-01 0.02473215
 [4,] 9.403924e-01 0.05960757
 [5,] 9.712252e-01 0.02877481
 [6,] 8.271040e-01 0.17289602
 [7,] 9.775643e-01 0.02243569
 [8,] 9.795016e-01 0.02049839
 [9,] 9.745942e-01 0.02540581
[10,] 9.586991e-01 0.04130091
[11,] 9.793596e-01 0.02064043
[12,] 9.793772e-01 0.02062281
[13,] 9.810873e-01 0.01891269
[14,] 9.791420e-01 0.02085803
[15,] 9.795508e-01 0.02044917
[16,] 9.635848e-01 0.03641519
[17,] 9.737065e-01 0.02629352
[18,] 9.777421e-01 0.02225791
[19,] 9.720618e-01 0.02793822
[20,] 9.789589e-01 0.02104114
[21,] 8.908564e-01 0.10914359
[22,] 9.767104e-01 0.02328955
[23,] 9.604218e-01 0.03957818
[24,] 9.771452e-01 0.02285475
[25,] 9.701997e-01 0.02980033
[26,] 9.789785e-01 0.02102155
[27,] 9.100903e-01 0.08990968
[28,] 9.569536e-01 0.04304644
[29,] 8.337245e-01 0.16627550
[30,] 8.918259e-01 0.10817412
[31,] 9.785076e-01 0.02149239
[32,] 9.795580e-01 0.02044199
[33,] 9.790679e-01 0.02093214
[34,] 9.795597e-01 0.02044034
[35,] 9.711326e-01 0.02886741
[36,] 9.784339e-01 0.02156611
[37,] 9.791147e-01 0.02088532
[38,] 9.792033e-01 0.02079673
[39,] 9.204902e-01 0.07950980
[40,] 3.452179e-08 0.99999997
[41,] 9.673151e-01 0.03268487
[42,] 9.694155e-01 0.03058454
[43,] 9.785536e-01 0.02144635
[44,] 9.607354e-01 0.03926462
[45,] 9.794083e-01 0.02059168
[46,] 9.783383e-01 0.02166168
[47,] 9.755564e-01 0.02444360
[48,] 9.024635e-01 0.09753649
[49,] 9.579118e-01 0.04208825
[50,] 9.786131e-01 0.02138692
[51,] 9.774283e-01 0.02257172
[52,] 9.787646e-01 0.02123539
[53,] 9.765622e-01 0.02343783
[54,] 9.758839e-01 0.02411610
[55,] 9.409051e-01 0.05909490
[56,] 9.685618e-01 0.03143823
[57,] 9.795124e-01 0.02048761
[58,] 9.739294e-01 0.02607058
[59,] 3.028805e-01 0.69711950
[60,] 9.771700e-01 0.02283001
[61,] 9.737086e-01 0.02629142
[62,] 9.763191e-01 0.02368093
[63,] 9.297277e-01 0.07027235
[64,] 9.285247e-01 0.07147534
[65,] 9.714195e-01 0.02858048
[66,] 9.751724e-01 0.02482758
[67,] 9.665434e-01 0.03345658
[68,] 9.729372e-01 0.02706278
[69,] 9.792159e-01 0.02078406
[70,] 9.773606e-01 0.02263938
[71,] 9.749004e-01 0.02509964
[72,] 8.933618e-01 0.10663822
[73,] 9.794431e-01 0.02055685
[74,] 9.771537e-01 0.02284626
[75,] 9.479170e-01 0.05208302
[76,] 9.624196e-01 0.03758042
[77,] 9.792936e-01 0.02070639
[78,] 9.763918e-01 0.02360824
[79,] 9.726004e-01 0.02739960
[80,] 8.700579e-01 0.12994214
[81,] 9.756382e-01 0.02436182
[82,] 9.792104e-01 0.02078957
[83,] 9.809392e-01 0.01906082
[84,] 9.649717e-01 0.03502829
[85,] 9.772124e-01 0.02278764
[86,] 9.634657e-01 0.03653431
[87,] 9.450680e-01 0.05493204
[88,] 9.710827e-01 0.02891733

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

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

$permut.pc.stepwise.qda$best.pda$training.label
 [1] CTL CTL PHO PHO CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL PHO CTL CTL
[29] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[57] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL
[85] 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  79   7
   PHO   1   1
attr(,"error")
[1] 0.0909091


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

$permut.pc.stepwise.qda$best.vars
[1] 1

$permut.pc.stepwise.qda$best.var.names
[1] "Comp.1"

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

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

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


$max.p
[1] 8

$errors
  stepwise.lda pc.stepwise.lda permut.stepwise.lda permut.pc.stepwise.lda stepwise.qda pc.stepwise.qda
1   0.02272727      0.02272727          0.07954545             0.09090909   0.02272727      0.01136364
2   0.01136364      0.02272727          0.07954545             0.07954545   0.01136364      0.02272727
3   0.01136364      0.02272727          0.07954545             0.07954545   0.02272727      0.03409091
4   0.02272727      0.02272727          0.07954545             0.07954545   0.01136364      0.01136364
5   0.02272727      0.02272727          0.07954545             0.07954545   0.02272727      0.02272727
6   0.02272727      0.02272727          0.09090909             0.09090909           NA              NA
7   0.02272727      0.02272727          0.10227273             0.09090909           NA              NA
8   0.02272727      0.02272727          0.10227273             0.10227273           NA              NA
  permut.stepwise.qda permut.pc.stepwise.qda
1           0.1022727              0.0909091
2           0.1022727              0.1250000
3           0.0909091              0.1136364
4           0.1250000              0.1022727
5           0.1363636              0.1022727
6                  NA                     NA
7                  NA                     NA
8                  NA                     NA

$legend.labels
[1] "LDA"                   "LDA with PC"           "LDA, permuted"         "LDA with PC, permuted"
[5] "QDA"                   "QDA with PC"           "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    5 0.07954545      80       0       7       1
permut.pc.stepwise.lda 5 0.07954545      80       0       7       1
stepwise.qda           4 0.01136364      80       0       1       7
pc.stepwise.qda        4 0.01136364      80       0       1       7
permut.stepwise.qda    3 0.09090909      80       0       8       0
permut.pc.stepwise.qda 1 0.09090909      79       1       7       1

$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 0.02272727

$best.pda$confusion.table
  step              error added.var                      added.var.name CTL.CTL CTL.PHO PHO.CTL PHO.PHO
1    1 0.0227272727272727         1 Low.Pi_vs_High.Pi_in_WT_.NBW7._exp1      80       0       2       6
2    2 0.0113636363636364         5                         pho80_vs_WT      80       0       1       7
3    3 0.0113636363636364         2 Low.Pi_vs_High.Pi_in_WT_.NBW7._exp2      80       0       1       7
4    4 0.0227272727272727         3   Low.Pi_vs_High.Pi_in_WT_.DBY7286.      80       0       2       6
5    5 0.0227272727272727         4                         PHO4c_vs_WT      80       0       2       6
6    6 0.0227272727272727         6                         pho85_vs_WT      80       0       2       6
7    7 0.0227272727272727         7                   PHO81c_vs_WT_exp1      80       0       2       6
8    8 0.0227272727272727         8                   PHO81c_vs_WT_exp2      80       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 CTL CTL PHO CTL CTL CTL CTL CTL CTL
[29] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL
[57] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[85] 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" "YBR093C" "YBR115C" "YBR184W" "YBR296C"
[12] "YCL018W" "YDL131W" "YDL182W" "YDL205C" "YDL210W" "YDR011W" "YDR044W" "YDR234W" "YDR285W" "YDR406W" "YDR481C"
[23] "YEL021W" "YEL039C" "YER026C" "YER086W" "YER179W" "YGL009C" "YGL073W" "YGL213C" "YGR019W" "YGR044C" "YGR088W"
[34] "YGR121C" "YGR157W" "YGR233C" "YGR281W" "YHL022C" "YHR007C" "YHR008C" "YHR014W" "YHR037W" "YHR136C" "YHR153C"
[45] "YIL015W" "YIL072W" "YIR034C" "YJL106W" "YJL117W" "YJL153C" "YJL219W" "YJR048W" "YJR073C" "YJR094C" "YJR152W"
[56] "YKL182W" "YKL216W" "YKR039W" "YLR081W" "YLR142W" "YLR263W" "YLR329W" "YLR420W" "YLR438W" "YML051W" "YML054C"
[67] "YML075C" "YML123C" "YMR108W" "YMR133W" "YNL052W" "YNL104C" "YNL142W" "YNL210W" "YNR001C" "YNR050C" "YOL006C"
[78] "YOR065W" "YOR120W" "YOR153W" "YOR328W" "YOR351C" "YOR375C" "YPL111W" "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 CTL CTL PHO CTL CTL CTL CTL CTL CTL
[29] CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL
[57] CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL PHO CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL CTL
[85] 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"                         "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


