L2 Penalty

J. Taroni 2018

We’ve been asked to clarify why an L2 penalty is used on the PLIER B matrix.

We’ll see what happens in practice if we set the L2 parameter to zero.

Let’s work with the data that are 500 randomly selected samples from recount2; this is out of convenience, as the computational requirements will be relatively light.

The main PLIER function, for the version of PLIER we’ve used, begins here: https://github.com/wgmao/PLIER/blob/a2d4a2aa343f9ed4b9b945c04326bebd31533d4d/R/Allfuncs.R#L227

Set up

`%>%` <- dplyr::`%>%`
library(PLIER)

Loading required package: RColorBrewer
Loading required package: gplots

Attaching package: ‘gplots’

The following object is masked from ‘package:stats’:

    lowess

Loading required package: pheatmap
Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-13

Loading required package: knitr
Loading required package: rsvd
Loading required package: qvalue

We’ll need GetPathwayCoverage

source(file.path("util", "plier_util.R"))

Directories

Plot and results directories specifically for this notebook.

# plot and result directory setup for this notebook
plot.dir <- file.path("plots", "39")
dir.create(plot.dir, recursive = TRUE, showWarnings = FALSE)
results.dir <- file.path("results", "39")
dir.create(results.dir, recursive = TRUE, showWarnings = FALSE)

Read in data

Working only with n = 500 here.

models.file <- file.path("models", "subsampled_recount2_PLIER_model_500.RDS")
models.list <- readRDS(models.file)

Get the prior information matrix used with the subsampling experiments.

recount.prepped.data <- readRDS(file.path("data", "recount2_PLIER_data", 
                                          "recount_data_prep_PLIER.RDS"))
pathway.mat <- recount.prepped.data$all.paths.cm
rm(recount.prepped.data)

Main

What constants were used originally (calculated from SVD)?

lapply(models.list, function(x) x$PLIER$L1)

$`2876`
[1] 77.02955

$`7883`
[1] 75.08367

$`4089`
[1] 79.52204

$`8828`
[1] 66.83478

$`9401`
[1] 82.35129

lapply(models.list, function(x) x$PLIER$L2)

$`2876`
[1] 154.0591

$`7883`
[1] 150.1673

$`4089`
[1] 159.0441

$`8828`
[1] 133.6696

$`9401`
[1] 164.7026

These are the automatically selected values.

Training with L2 = 0

A custom function for setting L2 to zero.

# plier.repeat is a list with the elements exprs (a gene expression matrix) and
# PLIER (output of PLIER); it is a repeat from script/subsampling_PLIER.R.
# use PLIER results as input to a new PLIER model, where we use the k, L1, 
# priorMat, and expression from a repeat, BUT set L2 = 0
# only intended to be used in this environment (need pathway.)
SetL2Zero <- function(plier.repeat) {
  results <- PLIER::PLIER(data = as.matrix(plier.repeat$exprs),
                          priorMat = pathway.mat,
                          k = nrow(plier.repeat$PLIER$B),
                          L1 = plier.repeat$PLIER$L1,
                          L2 = 0,
                          trace = TRUE)
  message("\n\n")
  return(results)
}

Perform the training and save the results to file (they will be small enough to track with Git LFS).

penalty.zero.list <- lapply(models.list, SetL2Zero)

Removing 1 pathways with too few genesComputing SVD
Done
errorY (SVD based:best possible) = 0.5382
iter1 errorY= 0.6311, Bdiff= 0.2755, Bkappa=16.12
iter2 errorY= 0.5784, Bdiff= 0.06306, Bkappa=24.56
iter3 errorY= 0.5647, Bdiff= 0.02682, Bkappa=31.87
iter4 errorY= 0.5584, Bdiff= 0.01488, Bkappa=37.9
iter5 errorY= 0.5547, Bdiff= 0.009417, Bkappa=43.41
iter6 errorY= 0.5523, Bdiff= 0.0065, Bkappa=48.37
iter7 errorY= 0.5506, Bdiff= 0.004775, Bkappa=52.86
iter8 errorY= 0.5494, Bdiff= 0.003677, Bkappa=57.35
iter9 errorY= 0.5484, Bdiff= 0.00294, Bkappa=61.64
iter10 errorY= 0.5477, Bdiff= 0.002405, Bkappa=65.55
iter11 errorY= 0.5471, Bdiff= 0.001986, Bkappa=69.03
iter12 errorY= 0.5466, Bdiff= 0.001652, Bkappa=72.08
iter13 errorY= 0.5462, Bdiff= 0.001394, Bkappa=74.8
iter14 errorY= 0.5458, Bdiff= 0.001204, Bkappa=75.39
iter15 errorY= 0.5455, Bdiff= 0.001058, Bkappa=77.68
iter16 errorY= 0.5452, Bdiff= 0.0009388, Bkappa=79.76
iter17 errorY= 0.545, Bdiff= 0.0008405, Bkappa=81.65
iter18 errorY= 0.5448, Bdiff= 0.0007585, Bkappa=83.49
iter19 errorY= 0.5446, Bdiff= 0.0006915, Bkappa=85.18
Updating L3, current fraction= 0, target=0.7
L3 is set to 0.00052 in 15 iterations
iter20 errorY= 0.5445, prior information ratio= 0, Bdiff= 0.0006345, Bkappa=86.66;pos. col. U=21
iter21 errorY= 0.5443, prior information ratio= 0, Bdiff= 0.0005846, Bkappa=87.93;pos. col. U=21
iter22 errorY= 0.5442, prior information ratio= 0, Bdiff= 0.0005416, Bkappa=89.13;pos. col. U=21
iter23 errorY= 0.544, prior information ratio= 0, Bdiff= 0.0005047, Bkappa=90.45;pos. col. U=21
iter24 errorY= 0.5439, prior information ratio= 0, Bdiff= 0.0004729, Bkappa=91.73;pos. col. U=21
iter25 errorY= 0.5438, prior information ratio= 0, Bdiff= 0.0004428, Bkappa=92.88;pos. col. U=20
iter26 errorY= 0.5437, prior information ratio= 0, Bdiff= 0.0004156, Bkappa=93.89;pos. col. U=20
iter27 errorY= 0.5436, prior information ratio= 0, Bdiff= 0.0003916, Bkappa=94.79;pos. col. U=20
iter28 errorY= 0.5435, prior information ratio= 0, Bdiff= 0.0003701, Bkappa=95.57;pos. col. U=20
iter29 errorY= 0.5434, prior information ratio= 0, Bdiff= 0.0003507, Bkappa=96.26;pos. col. U=20
iter30 errorY= 0.5433, prior information ratio= 0, Bdiff= 0.0003329, Bkappa=96.87;pos. col. U=20
iter31 errorY= 0.5432, prior information ratio= 0, Bdiff= 0.000316, Bkappa=97.41;pos. col. U=20
iter32 errorY= 0.5431, prior information ratio= 0, Bdiff= 0.0002998, Bkappa=97.88;pos. col. U=20
iter33 errorY= 0.543, prior information ratio= 0, Bdiff= 0.0002844, Bkappa=98.3;pos. col. U=20
iter34 errorY= 0.5429, prior information ratio= 0, Bdiff= 0.0002698, Bkappa=98.7;pos. col. U=19
iter35 errorY= 0.5429, prior information ratio= 0, Bdiff= 0.0002556, Bkappa=99.21;pos. col. U=19
iter36 errorY= 0.5428, prior information ratio= 0, Bdiff= 0.0002414, Bkappa=99.68;pos. col. U=19
iter37 errorY= 0.5427, prior information ratio= 0, Bdiff= 0.0002279, Bkappa=100.6;pos. col. U=19
iter38 errorY= 0.5427, prior information ratio= 0, Bdiff= 0.0002153, Bkappa=101.1;pos. col. U=19
iter39 errorY= 0.5426, prior information ratio= 0, Bdiff= 0.0002034, Bkappa=101.4;pos. col. U=19
Updating L3, current fraction= 0.6333, target=0.7
L3 is set to 0.000455 in 3 iterations
iter40 errorY= 0.5426, prior information ratio= 0, Bdiff= 0.0001925, Bkappa=101.8;pos. col. U=20
iter41 errorY= 0.5425, prior information ratio= 0, Bdiff= 0.0001821, Bkappa=102.1;pos. col. U=20
iter42 errorY= 0.5425, prior information ratio= 0, Bdiff= 0.0001727, Bkappa=102.4;pos. col. U=20
iter43 errorY= 0.5424, prior information ratio= 0, Bdiff= 0.0001643, Bkappa=102.7;pos. col. U=20
iter44 errorY= 0.5424, prior information ratio= 0, Bdiff= 0.0001566, Bkappa=101.8;pos. col. U=20
iter45 errorY= 0.5423, prior information ratio= 0, Bdiff= 0.0001496, Bkappa=102;pos. col. U=20
iter46 errorY= 0.5423, prior information ratio= 0, Bdiff= 0.0001433, Bkappa=102.2;pos. col. U=20
iter47 errorY= 0.5423, prior information ratio= 0, Bdiff= 0.0001376, Bkappa=102.4;pos. col. U=20
iter48 errorY= 0.5422, prior information ratio= 0, Bdiff= 0.0001321, Bkappa=102.5;pos. col. U=20
iter49 errorY= 0.5422, prior information ratio= 0, Bdiff= 0.000127, Bkappa=102.6;pos. col. U=20
iter50 errorY= 0.5422, prior information ratio= 0, Bdiff= 0.0001224, Bkappa=102.7;pos. col. U=20
iter51 errorY= 0.5421, prior information ratio= 0, Bdiff= 0.000118, Bkappa=102.8;pos. col. U=20
iter52 errorY= 0.5421, prior information ratio= 0, Bdiff= 0.0001139, Bkappa=102.9;pos. col. U=20
iter53 errorY= 0.5421, prior information ratio= 0, Bdiff= 0.0001101, Bkappa=102.9;pos. col. U=20
iter54 errorY= 0.5421, prior information ratio= 0, Bdiff= 0.0001064, Bkappa=103;pos. col. U=20
iter55 errorY= 0.542, prior information ratio= 0, Bdiff= 0.000103, Bkappa=103;pos. col. U=20
iter56 errorY= 0.542, prior information ratio= 0, Bdiff= 9.979e-05, Bkappa=103.1;pos. col. U=20
iter57 errorY= 0.542, prior information ratio= 0, Bdiff= 9.68e-05, Bkappa=103.4;pos. col. U=20
iter58 errorY= 0.5419, prior information ratio= 0, Bdiff= 9.4e-05, Bkappa=103.7;pos. col. U=20
iter59 errorY= 0.5419, prior information ratio= 0, Bdiff= 9.134e-05, Bkappa=104;pos. col. U=20
Updating L3, current fraction= 0.6667, target=0.7
L3 not changed
iter60 errorY= 0.5419, prior information ratio= 0, Bdiff= 8.887e-05, Bkappa=104.4;pos. col. U=20
iter61 errorY= 0.5419, prior information ratio= 0, Bdiff= 8.653e-05, Bkappa=104.7;pos. col. U=20
iter62 errorY= 0.5419, prior information ratio= 0, Bdiff= 8.43e-05, Bkappa=105;pos. col. U=20
iter63 errorY= 0.5418, prior information ratio= 0, Bdiff= 8.221e-05, Bkappa=105.3;pos. col. U=20
iter64 errorY= 0.5418, prior information ratio= 0, Bdiff= 8.034e-05, Bkappa=105.5;pos. col. U=20
iter65 errorY= 0.5418, prior information ratio= 0, Bdiff= 7.861e-05, Bkappa=105.8;pos. col. U=20
iter66 errorY= 0.5418, prior information ratio= 0, Bdiff= 7.699e-05, Bkappa=106.1;pos. col. U=20
iter67 errorY= 0.5417, prior information ratio= 0, Bdiff= 7.552e-05, Bkappa=106.3;pos. col. U=19
iter68 errorY= 0.5417, prior information ratio= 0, Bdiff= 7.421e-05, Bkappa=106.6;pos. col. U=19
iter69 errorY= 0.5417, prior information ratio= 0, Bdiff= 7.292e-05, Bkappa=106.9;pos. col. U=19
iter70 errorY= 0.5417, prior information ratio= 0, Bdiff= 7.17e-05, Bkappa=107.2;pos. col. U=18
iter71 errorY= 0.5417, prior information ratio= 0, Bdiff= 7.063e-05, Bkappa=107.5;pos. col. U=18
iter72 errorY= 0.5416, prior information ratio= 0, Bdiff= 6.961e-05, Bkappa=67.28;pos. col. U=18
iter73 errorY= 0.5416, prior information ratio= 0, Bdiff= 6.866e-05, Bkappa=67.44;pos. col. U=18
iter74 errorY= 0.5416, prior information ratio= 0, Bdiff= 6.776e-05, Bkappa=67.6;pos. col. U=18
iter75 errorY= 0.5416, prior information ratio= 0, Bdiff= 6.686e-05, Bkappa=67.75;pos. col. U=17
iter76 errorY= 0.5416, prior information ratio= 0, Bdiff= 6.601e-05, Bkappa=67.91;pos. col. U=17
iter77 errorY= 0.5416, prior information ratio= 0, Bdiff= 6.513e-05, Bkappa=97.03;pos. col. U=17
iter78 errorY= 0.5416, prior information ratio= 0, Bdiff= 6.421e-05, Bkappa=97.27;pos. col. U=17
iter79 errorY= 0.5415, prior information ratio= 0, Bdiff= 6.327e-05, Bkappa=97.51;pos. col. U=17
Updating L3, current fraction= 0.5667, target=0.7
L3 is set to 0.000399 in 3 iterations
iter80 errorY= 0.5415, prior information ratio= 0, Bdiff= 6.234e-05, Bkappa=97.75;pos. col. U=22
iter81 errorY= 0.5415, prior information ratio= 0, Bdiff= 6.143e-05, Bkappa=97.99;pos. col. U=22
iter82 errorY= 0.5415, prior information ratio= 0, Bdiff= 6.056e-05, Bkappa=98.23;pos. col. U=22
iter83 errorY= 0.5415, prior information ratio= 0, Bdiff= 5.972e-05, Bkappa=98.5;pos. col. U=22
iter84 errorY= 0.5415, prior information ratio= 0, Bdiff= 5.892e-05, Bkappa=98.78;pos. col. U=22
iter85 errorY= 0.5415, prior information ratio= 0, Bdiff= 5.817e-05, Bkappa=99.06;pos. col. U=22
iter86 errorY= 0.5414, prior information ratio= 0, Bdiff= 5.743e-05, Bkappa=99.34;pos. col. U=22
iter87 errorY= 0.5414, prior information ratio= 0, Bdiff= 5.666e-05, Bkappa=99.62;pos. col. U=22
iter88 errorY= 0.5414, prior information ratio= 0, Bdiff= 5.588e-05, Bkappa=99.91;pos. col. U=22
iter89 errorY= 0.5414, prior information ratio= 0, Bdiff= 5.509e-05, Bkappa=100.2;pos. col. U=22
iter90 errorY= 0.5414, prior information ratio= 0, Bdiff= 5.434e-05, Bkappa=100.5;pos. col. U=22
iter91 errorY= 0.5414, prior information ratio= 0, Bdiff= 5.358e-05, Bkappa=100.8;pos. col. U=22
iter92 errorY= 0.5414, prior information ratio= 0, Bdiff= 5.283e-05, Bkappa=101.2;pos. col. U=22
iter93 errorY= 0.5414, prior information ratio= 0, Bdiff= 5.211e-05, Bkappa=101.5;pos. col. U=22
iter94 errorY= 0.5414, prior information ratio= 0, Bdiff= 5.137e-05, Bkappa=101.8;pos. col. U=21
iter95 errorY= 0.5413, prior information ratio= 0, Bdiff= 5.065e-05, Bkappa=102.1;pos. col. U=21
iter96 errorY= 0.5413, prior information ratio= 0, Bdiff= 4.997e-05, Bkappa=102.4;pos. col. U=21
iter97 errorY= 0.5413, prior information ratio= 0, Bdiff= 4.935e-05, Bkappa=102.7;pos. col. U=21
iter98 errorY= 0.5413, prior information ratio= 0, Bdiff= 4.876e-05, Bkappa=103.1;pos. col. U=21
iter99 errorY= 0.5413, prior information ratio= 0, Bdiff= 4.821e-05, Bkappa=103.4;pos. col. U=21
Updating L3, current fraction= 0.7, target=0.7
L3 not changed
iter100 errorY= 0.5413, prior information ratio= 0, Bdiff= 4.768e-05, Bkappa=103.7;pos. col. U=21
iter101 errorY= 0.5413, prior information ratio= 0, Bdiff= 4.723e-05, Bkappa=104.1;pos. col. U=20
iter102 errorY= 0.5413, prior information ratio= 0, Bdiff= 4.679e-05, Bkappa=104.6;pos. col. U=20
iter103 errorY= 0.5413, prior information ratio= 0, Bdiff= 4.637e-05, Bkappa=105.1;pos. col. U=20
iter104 errorY= 0.5413, prior information ratio= 0, Bdiff= 4.595e-05, Bkappa=105.5;pos. col. U=20
iter105 errorY= 0.5413, prior information ratio= 0, Bdiff= 4.56e-05, Bkappa=106;pos. col. U=20
iter106 errorY= 0.5413, prior information ratio= 0, Bdiff= 4.526e-05, Bkappa=106.5;pos. col. U=20
iter107 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.493e-05, Bkappa=107;pos. col. U=20
iter108 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.459e-05, Bkappa=107.5;pos. col. U=20
iter109 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.427e-05, Bkappa=119.6;pos. col. U=20
iter110 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.395e-05, Bkappa=120.1;pos. col. U=20
iter111 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.361e-05, Bkappa=120.7;pos. col. U=19
iter112 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.329e-05, Bkappa=121.2;pos. col. U=19
iter113 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.302e-05, Bkappa=121.8;pos. col. U=19
iter114 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.276e-05, Bkappa=122.3;pos. col. U=19
iter115 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.251e-05, Bkappa=122.9;pos. col. U=19
iter116 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.227e-05, Bkappa=123.6;pos. col. U=19
iter117 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.206e-05, Bkappa=124.3;pos. col. U=19
iter118 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.187e-05, Bkappa=124.9;pos. col. U=18
iter119 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.17e-05, Bkappa=125.5;pos. col. U=18
Updating L3, current fraction= 0.6, target=0.7
L3 is set to 0.00035 in 3 iterations
iter120 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.155e-05, Bkappa=126.2;pos. col. U=22
iter121 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.139e-05, Bkappa=126.8;pos. col. U=22
iter122 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.122e-05, Bkappa=127.4;pos. col. U=22
iter123 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.105e-05, Bkappa=128.1;pos. col. U=22
iter124 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.087e-05, Bkappa=128.7;pos. col. U=22
iter125 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.068e-05, Bkappa=129.3;pos. col. U=21
iter126 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.051e-05, Bkappa=130;pos. col. U=20
iter127 errorY= 0.5411, prior information ratio= 0, Bdiff= 4.034e-05, Bkappa=130.6;pos. col. U=20
iter128 errorY= 0.5411, prior information ratio= 0, Bdiff= 4.017e-05, Bkappa=131.3;pos. col. U=20
iter129 errorY= 0.5411, prior information ratio= 0, Bdiff= 4e-05, Bkappa=131.9;pos. col. U=20
iter130 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.984e-05, Bkappa=132.6;pos. col. U=20
iter131 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.968e-05, Bkappa=133.2;pos. col. U=20
iter132 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.953e-05, Bkappa=133.9;pos. col. U=20
iter133 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.94e-05, Bkappa=129.5;pos. col. U=20
iter134 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.927e-05, Bkappa=130.1;pos. col. U=20
iter135 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.915e-05, Bkappa=135.9;pos. col. U=20
iter136 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.905e-05, Bkappa=136.6;pos. col. U=20
iter137 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.894e-05, Bkappa=137.3;pos. col. U=20
iter138 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.885e-05, Bkappa=138;pos. col. U=20
iter139 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.878e-05, Bkappa=138.7;pos. col. U=20
Updating L3, current fraction= 0.6667, target=0.7
L3 not changed
iter140 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.871e-05, Bkappa=139.4;pos. col. U=20
iter141 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.864e-05, Bkappa=140.1;pos. col. U=20
iter142 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.858e-05, Bkappa=140.8;pos. col. U=20
iter143 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.851e-05, Bkappa=141.5;pos. col. U=20
iter144 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.844e-05, Bkappa=142.2;pos. col. U=20
iter145 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.836e-05, Bkappa=142.9;pos. col. U=20
iter146 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.827e-05, Bkappa=143.6;pos. col. U=20
iter147 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.819e-05, Bkappa=144.4;pos. col. U=20
iter148 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.812e-05, Bkappa=145.1;pos. col. U=20
iter149 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.806e-05, Bkappa=145.8;pos. col. U=20
iter150 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.799e-05, Bkappa=146.6;pos. col. U=20
iter151 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.793e-05, Bkappa=147.3;pos. col. U=20
iter152 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.786e-05, Bkappa=148;pos. col. U=20
iter153 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.78e-05, Bkappa=151.1;pos. col. U=20
iter154 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.779e-05, Bkappa=151.8;pos. col. U=20
iter155 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.778e-05, Bkappa=131.9;pos. col. U=20
iter156 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.782e-05, Bkappa=132.5;pos. col. U=20
iter157 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.791e-05, Bkappa=133.2;pos. col. U=20
iter158 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.801e-05, Bkappa=133.9;pos. col. U=20
iter159 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.812e-05, Bkappa=134.5;pos. col. U=20
Updating L3, current fraction= 0.6667, target=0.7
L3 not changed
iter160 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.825e-05, Bkappa=135.2;pos. col. U=20
iter161 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.838e-05, Bkappa=135.9;pos. col. U=20
iter162 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.85e-05, Bkappa=136.5;pos. col. U=20
iter163 errorY= 0.5411, prior information ratio= 0, Bdiff= 3.861e-05, Bkappa=137.2;pos. col. U=20
iter164 errorY= 0.5412, prior information ratio= 0, Bdiff= 3.874e-05, Bkappa=137.9;pos. col. U=20
iter165 errorY= 0.5412, prior information ratio= 0, Bdiff= 3.886e-05, Bkappa=138.6;pos. col. U=20
iter166 errorY= 0.5412, prior information ratio= 0, Bdiff= 3.897e-05, Bkappa=139.3;pos. col. U=20
iter167 errorY= 0.5412, prior information ratio= 0, Bdiff= 3.907e-05, Bkappa=140;pos. col. U=20
iter168 errorY= 0.5412, prior information ratio= 0, Bdiff= 3.918e-05, Bkappa=140.7;pos. col. U=20
iter169 errorY= 0.5412, prior information ratio= 0, Bdiff= 3.933e-05, Bkappa=141.4;pos. col. U=20
iter170 errorY= 0.5412, prior information ratio= 0, Bdiff= 3.948e-05, Bkappa=142.1;pos. col. U=20
iter171 errorY= 0.5412, prior information ratio= 0, Bdiff= 3.967e-05, Bkappa=142.8;pos. col. U=20
iter172 errorY= 0.5412, prior information ratio= 0, Bdiff= 3.985e-05, Bkappa=143.5;pos. col. U=20
iter173 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.004e-05, Bkappa=144.2;pos. col. U=20
iter174 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.024e-05, Bkappa=156.1;pos. col. U=20
iter175 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.048e-05, Bkappa=156.8;pos. col. U=20
iter176 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.074e-05, Bkappa=157.6;pos. col. U=20
Bdiff is not decreasing
iter177 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.099e-05, Bkappa=158.3;pos. col. U=20
Bdiff is not decreasing
iter178 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.128e-05, Bkappa=159.1;pos. col. U=19
Bdiff is not decreasing
iter179 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.158e-05, Bkappa=159.8;pos. col. U=19
Bdiff is not decreasing
Updating L3, current fraction= 0.6333, target=0.7
L3 is set to 0.000306 in 3 iterations
iter180 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.19e-05, Bkappa=160.6;pos. col. U=21
Bdiff is not decreasing
iter181 errorY= 0.5412, prior information ratio= 0, Bdiff= 4.222e-05, Bkappa=161.4;pos. col. U=21
Bdiff is not decreasing
converged at  iteration 181 Bdiff is not decreasing
There are 18  LVs with AUC>0.70



Removing 1 pathways with too few genesComputing SVD
Done
errorY (SVD based:best possible) = 0.5582
iter1 errorY= 0.6301, Bdiff= 0.2436, Bkappa=11.76
iter2 errorY= 0.5885, Bdiff= 0.04257, Bkappa=16.54
iter3 errorY= 0.578, Bdiff= 0.0169, Bkappa=19.46
iter4 errorY= 0.5731, Bdiff= 0.009447, Bkappa=21.54
iter5 errorY= 0.5703, Bdiff= 0.006217, Bkappa=24.18
iter6 errorY= 0.5684, Bdiff= 0.004475, Bkappa=26.53
iter7 errorY= 0.567, Bdiff= 0.003253, Bkappa=28.56
iter8 errorY= 0.566, Bdiff= 0.002392, Bkappa=30.25
iter9 errorY= 0.5652, Bdiff= 0.001818, Bkappa=31.64
iter10 errorY= 0.5647, Bdiff= 0.001423, Bkappa=32.79
iter11 errorY= 0.5642, Bdiff= 0.001145, Bkappa=33.74
iter12 errorY= 0.5638, Bdiff= 0.000948, Bkappa=34.54
iter13 errorY= 0.5635, Bdiff= 0.0008057, Bkappa=35.22
iter14 errorY= 0.5632, Bdiff= 0.0007011, Bkappa=35.81
iter15 errorY= 0.563, Bdiff= 0.0006208, Bkappa=36.31
iter16 errorY= 0.5628, Bdiff= 0.0005589, Bkappa=36.75
iter17 errorY= 0.5626, Bdiff= 0.0005114, Bkappa=37.11
iter18 errorY= 0.5624, Bdiff= 0.000473, Bkappa=37.4
iter19 errorY= 0.5623, Bdiff= 0.0004407, Bkappa=37.65
Updating L3, current fraction= 0, target=0.7
L3 is set to 0.000489 in 11 iterations
iter20 errorY= 0.5622, prior information ratio= 0, Bdiff= 0.0004136, Bkappa=37.87;pos. col. U=20
iter21 errorY= 0.562, prior information ratio= 0, Bdiff= 0.0003908, Bkappa=38.06;pos. col. U=20
iter22 errorY= 0.5619, prior information ratio= 0, Bdiff= 0.0003714, Bkappa=38.28;pos. col. U=20
iter23 errorY= 0.5618, prior information ratio= 0, Bdiff= 0.0003542, Bkappa=38.52;pos. col. U=20
iter24 errorY= 0.5618, prior information ratio= 0, Bdiff= 0.0003392, Bkappa=38.74;pos. col. U=20
iter25 errorY= 0.5617, prior information ratio= 0, Bdiff= 0.0003261, Bkappa=38.95;pos. col. U=20
iter26 errorY= 0.5616, prior information ratio= 0, Bdiff= 0.0003142, Bkappa=39.13;pos. col. U=20
iter27 errorY= 0.5615, prior information ratio= 0, Bdiff= 0.0003029, Bkappa=39.3;pos. col. U=19
iter28 errorY= 0.5615, prior information ratio= 0, Bdiff= 0.0002925, Bkappa=39.46;pos. col. U=19
iter29 errorY= 0.5614, prior information ratio= 0, Bdiff= 0.0002827, Bkappa=39.6;pos. col. U=16
iter30 errorY= 0.5613, prior information ratio= 0, Bdiff= 0.0002734, Bkappa=39.73;pos. col. U=14
iter31 errorY= 0.5613, prior information ratio= 0, Bdiff= 0.0002642, Bkappa=39.85;pos. col. U=14
iter32 errorY= 0.5612, prior information ratio= 0, Bdiff= 0.0002551, Bkappa=39.95;pos. col. U=11
iter33 errorY= 0.5612, prior information ratio= 0, Bdiff= 0.0002463, Bkappa=40.28;pos. col. U=11
iter34 errorY= 0.5611, prior information ratio= 0, Bdiff= 0.0002374, Bkappa=40.65;pos. col. U=10
iter35 errorY= 0.5611, prior information ratio= 0, Bdiff= 0.0002281, Bkappa=41;pos. col. U=10
iter36 errorY= 0.5611, prior information ratio= 0, Bdiff= 0.0002191, Bkappa=41.34;pos. col. U=10
iter37 errorY= 0.561, prior information ratio= 0, Bdiff= 0.0002101, Bkappa=41.68;pos. col. U=10
iter38 errorY= 0.561, prior information ratio= 0, Bdiff= 0.0002014, Bkappa=42.07;pos. col. U=10
iter39 errorY= 0.5609, prior information ratio= 0, Bdiff= 0.0001929, Bkappa=42.44;pos. col. U=10
Updating L3, current fraction= 0.3333, target=0.7
L3 is set to 0.000429 in 3 iterations
iter40 errorY= 0.5609, prior information ratio= 0, Bdiff= 0.0001845, Bkappa=42.79;pos. col. U=22
iter41 errorY= 0.5609, prior information ratio= 0, Bdiff= 0.0001763, Bkappa=43.12;pos. col. U=21
iter42 errorY= 0.5608, prior information ratio= 0, Bdiff= 0.0001684, Bkappa=43.43;pos. col. U=21
iter43 errorY= 0.5608, prior information ratio= 0, Bdiff= 0.0001609, Bkappa=43.71;pos. col. U=20
iter44 errorY= 0.5608, prior information ratio= 0, Bdiff= 0.0001536, Bkappa=43.97;pos. col. U=18
iter45 errorY= 0.5608, prior information ratio= 0, Bdiff= 0.0001468, Bkappa=44.22;pos. col. U=18
iter46 errorY= 0.5607, prior information ratio= 0, Bdiff= 0.0001404, Bkappa=44.45;pos. col. U=17
iter47 errorY= 0.5607, prior information ratio= 0, Bdiff= 0.0001341, Bkappa=44.66;pos. col. U=16
iter48 errorY= 0.5607, prior information ratio= 0, Bdiff= 0.0001282, Bkappa=44.86;pos. col. U=16
iter49 errorY= 0.5607, prior information ratio= 0, Bdiff= 0.0001226, Bkappa=45.04;pos. col. U=14
iter50 errorY= 0.5606, prior information ratio= 0, Bdiff= 0.0001173, Bkappa=45.21;pos. col. U=13
iter51 errorY= 0.5606, prior information ratio= 0, Bdiff= 0.0001124, Bkappa=43.32;pos. col. U=12
iter52 errorY= 0.5606, prior information ratio= 0, Bdiff= 0.0001079, Bkappa=43.46;pos. col. U=12
iter53 errorY= 0.5606, prior information ratio= 0, Bdiff= 0.0001035, Bkappa=43.6;pos. col. U=12
iter54 errorY= 0.5606, prior information ratio= 0, Bdiff= 9.941e-05, Bkappa=44.8;pos. col. U=12
iter55 errorY= 0.5606, prior information ratio= 0, Bdiff= 9.554e-05, Bkappa=44.93;pos. col. U=12
iter56 errorY= 0.5605, prior information ratio= 0, Bdiff= 9.187e-05, Bkappa=45.06;pos. col. U=12
iter57 errorY= 0.5605, prior information ratio= 0, Bdiff= 8.845e-05, Bkappa=45.17;pos. col. U=12
iter58 errorY= 0.5605, prior information ratio= 0, Bdiff= 8.52e-05, Bkappa=45.28;pos. col. U=12
iter59 errorY= 0.5605, prior information ratio= 0, Bdiff= 8.211e-05, Bkappa=45.49;pos. col. U=12
Updating L3, current fraction= 0.4, target=0.7
L3 is set to 0.000376 in 3 iterations
iter60 errorY= 0.5605, prior information ratio= 0, Bdiff= 7.923e-05, Bkappa=45.89;pos. col. U=22
iter61 errorY= 0.5605, prior information ratio= 0, Bdiff= 7.656e-05, Bkappa=46.28;pos. col. U=22
iter62 errorY= 0.5605, prior information ratio= 0, Bdiff= 7.403e-05, Bkappa=46.65;pos. col. U=22
iter63 errorY= 0.5604, prior information ratio= 0, Bdiff= 7.166e-05, Bkappa=47;pos. col. U=22
iter64 errorY= 0.5604, prior information ratio= 0, Bdiff= 6.943e-05, Bkappa=47.34;pos. col. U=21
iter65 errorY= 0.5604, prior information ratio= 0, Bdiff= 6.738e-05, Bkappa=47.67;pos. col. U=19
iter66 errorY= 0.5604, prior information ratio= 0, Bdiff= 6.542e-05, Bkappa=47.98;pos. col. U=18
iter67 errorY= 0.5604, prior information ratio= 0, Bdiff= 6.357e-05, Bkappa=48.31;pos. col. U=18
iter68 errorY= 0.5604, prior information ratio= 0, Bdiff= 6.179e-05, Bkappa=48.66;pos. col. U=18
iter69 errorY= 0.5604, prior information ratio= 0, Bdiff= 6.012e-05, Bkappa=48.99;pos. col. U=17
iter70 errorY= 0.5604, prior information ratio= 0, Bdiff= 5.853e-05, Bkappa=49.31;pos. col. U=17
iter71 errorY= 0.5604, prior information ratio= 0, Bdiff= 5.7e-05, Bkappa=44.13;pos. col. U=17
iter72 errorY= 0.5603, prior information ratio= 0, Bdiff= 5.553e-05, Bkappa=44.39;pos. col. U=17
iter73 errorY= 0.5603, prior information ratio= 0, Bdiff= 5.411e-05, Bkappa=44.63;pos. col. U=17
iter74 errorY= 0.5603, prior information ratio= 0, Bdiff= 5.276e-05, Bkappa=44.87;pos. col. U=16
iter75 errorY= 0.5603, prior information ratio= 0, Bdiff= 5.146e-05, Bkappa=45.1;pos. col. U=17
iter76 errorY= 0.5603, prior information ratio= 0, Bdiff= 5.024e-05, Bkappa=45.31;pos. col. U=17
iter77 errorY= 0.5603, prior information ratio= 0, Bdiff= 4.907e-05, Bkappa=45.52;pos. col. U=17
iter78 errorY= 0.5603, prior information ratio= 0, Bdiff= 4.796e-05, Bkappa=45.72;pos. col. U=17
iter79 errorY= 0.5603, prior information ratio= 0, Bdiff= 4.693e-05, Bkappa=45.91;pos. col. U=17
Updating L3, current fraction= 0.5667, target=0.7
L3 is set to 0.000352 in 4 iterations
iter80 errorY= 0.5603, prior information ratio= 0, Bdiff= 4.593e-05, Bkappa=46.09;pos. col. U=21
iter81 errorY= 0.5603, prior information ratio= 0, Bdiff= 4.496e-05, Bkappa=46.27;pos. col. U=21
iter82 errorY= 0.5603, prior information ratio= 0, Bdiff= 4.403e-05, Bkappa=46.43;pos. col. U=20
iter83 errorY= 0.5603, prior information ratio= 0, Bdiff= 4.312e-05, Bkappa=46.59;pos. col. U=20
iter84 errorY= 0.5603, prior information ratio= 0, Bdiff= 4.226e-05, Bkappa=46.74;pos. col. U=20
iter85 errorY= 0.5602, prior information ratio= 0, Bdiff= 4.144e-05, Bkappa=46.88;pos. col. U=20
iter86 errorY= 0.5602, prior information ratio= 0, Bdiff= 4.067e-05, Bkappa=47.02;pos. col. U=19
iter87 errorY= 0.5602, prior information ratio= 0, Bdiff= 3.994e-05, Bkappa=47.14;pos. col. U=19
iter88 errorY= 0.5602, prior information ratio= 0, Bdiff= 3.924e-05, Bkappa=47.28;pos. col. U=19
iter89 errorY= 0.5602, prior information ratio= 0, Bdiff= 3.856e-05, Bkappa=47.42;pos. col. U=19
iter90 errorY= 0.5602, prior information ratio= 0, Bdiff= 3.791e-05, Bkappa=53.6;pos. col. U=19
iter91 errorY= 0.5602, prior information ratio= 0, Bdiff= 3.73e-05, Bkappa=53.75;pos. col. U=19
iter92 errorY= 0.5602, prior information ratio= 0, Bdiff= 3.67e-05, Bkappa=53.89;pos. col. U=19
iter93 errorY= 0.5602, prior information ratio= 0, Bdiff= 3.612e-05, Bkappa=54.03;pos. col. U=18
iter94 errorY= 0.5602, prior information ratio= 0, Bdiff= 3.555e-05, Bkappa=54.16;pos. col. U=18
iter95 errorY= 0.5602, prior information ratio= 0, Bdiff= 3.499e-05, Bkappa=54.29;pos. col. U=18
iter96 errorY= 0.5602, prior information ratio= 0, Bdiff= 3.446e-05, Bkappa=54.41;pos. col. U=18
iter97 errorY= 0.5602, prior information ratio= 0, Bdiff= 3.395e-05, Bkappa=54.52;pos. col. U=17
iter98 errorY= 0.5602, prior information ratio= 0, Bdiff= 3.344e-05, Bkappa=54.63;pos. col. U=17
iter99 errorY= 0.5602, prior information ratio= 0, Bdiff= 3.295e-05, Bkappa=54.73;pos. col. U=17
Updating L3, current fraction= 0.5667, target=0.7
L3 is set to 0.000331 in 4 iterations
iter100 errorY= 0.5602, prior information ratio= 0, Bdiff= 3.246e-05, Bkappa=54.82;pos. col. U=22
iter101 errorY= 0.5602, prior information ratio= 0, Bdiff= 3.198e-05, Bkappa=54.91;pos. col. U=21
iter102 errorY= 0.5602, prior information ratio= 0, Bdiff= 3.152e-05, Bkappa=55;pos. col. U=21
iter103 errorY= 0.5602, prior information ratio= 0, Bdiff= 3.108e-05, Bkappa=55.08;pos. col. U=21
iter104 errorY= 0.5601, prior information ratio= 0, Bdiff= 3.065e-05, Bkappa=55.16;pos. col. U=21
iter105 errorY= 0.5601, prior information ratio= 0, Bdiff= 3.024e-05, Bkappa=55.23;pos. col. U=20
iter106 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.983e-05, Bkappa=55.33;pos. col. U=20
iter107 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.944e-05, Bkappa=55.42;pos. col. U=20
iter108 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.905e-05, Bkappa=55.51;pos. col. U=20
iter109 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.867e-05, Bkappa=55.59;pos. col. U=20
iter110 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.829e-05, Bkappa=55.67;pos. col. U=19
iter111 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.793e-05, Bkappa=52.11;pos. col. U=19
iter112 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.757e-05, Bkappa=52.17;pos. col. U=19
iter113 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.723e-05, Bkappa=52.23;pos. col. U=19
iter114 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.689e-05, Bkappa=52.29;pos. col. U=19
iter115 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.656e-05, Bkappa=52.34;pos. col. U=18
iter116 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.623e-05, Bkappa=52.38;pos. col. U=17
iter117 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.591e-05, Bkappa=52.43;pos. col. U=17
iter118 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.558e-05, Bkappa=52.47;pos. col. U=17
iter119 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.526e-05, Bkappa=52.5;pos. col. U=17
Updating L3, current fraction= 0.5667, target=0.7
L3 is set to 0.00031 in 4 iterations
iter120 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.496e-05, Bkappa=52.56;pos. col. U=22
iter121 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.466e-05, Bkappa=52.63;pos. col. U=22
iter122 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.437e-05, Bkappa=52.69;pos. col. U=22
iter123 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.408e-05, Bkappa=52.89;pos. col. U=21
iter124 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.38e-05, Bkappa=53.16;pos. col. U=21
iter125 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.353e-05, Bkappa=53.42;pos. col. U=21
iter126 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.327e-05, Bkappa=53.69;pos. col. U=20
iter127 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.301e-05, Bkappa=53.95;pos. col. U=20
iter128 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.276e-05, Bkappa=54.21;pos. col. U=20
iter129 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.252e-05, Bkappa=54.47;pos. col. U=20
iter130 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.23e-05, Bkappa=54.73;pos. col. U=20
iter131 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.208e-05, Bkappa=54.99;pos. col. U=20
iter132 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.187e-05, Bkappa=55.25;pos. col. U=20
iter133 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.166e-05, Bkappa=55.5;pos. col. U=20
iter134 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.146e-05, Bkappa=55.76;pos. col. U=19
iter135 errorY= 0.5601, prior information ratio= 0, Bdiff= 2.126e-05, Bkappa=56.01;pos. col. U=19
iter136 errorY= 0.56, prior information ratio= 0, Bdiff= 2.106e-05, Bkappa=56.27;pos. col. U=19
iter137 errorY= 0.56, prior information ratio= 0, Bdiff= 2.087e-05, Bkappa=56.52;pos. col. U=19
iter138 errorY= 0.56, prior information ratio= 0, Bdiff= 2.067e-05, Bkappa=56.77;pos. col. U=19
iter139 errorY= 0.56, prior information ratio= 0, Bdiff= 2.047e-05, Bkappa=57.02;pos. col. U=19
Updating L3, current fraction= 0.6333, target=0.7
L3 is set to 0.000291 in 4 iterations
iter140 errorY= 0.56, prior information ratio= 0, Bdiff= 2.027e-05, Bkappa=57.27;pos. col. U=22
iter141 errorY= 0.56, prior information ratio= 0, Bdiff= 2.009e-05, Bkappa=57.52;pos. col. U=22
iter142 errorY= 0.56, prior information ratio= 0, Bdiff= 1.99e-05, Bkappa=57.77;pos. col. U=22
iter143 errorY= 0.56, prior information ratio= 0, Bdiff= 1.972e-05, Bkappa=58.02;pos. col. U=22
iter144 errorY= 0.56, prior information ratio= 0, Bdiff= 1.953e-05, Bkappa=58.26;pos. col. U=22
iter145 errorY= 0.56, prior information ratio= 0, Bdiff= 1.935e-05, Bkappa=58.51;pos. col. U=22
iter146 errorY= 0.56, prior information ratio= 0, Bdiff= 1.917e-05, Bkappa=58.75;pos. col. U=22
iter147 errorY= 0.56, prior information ratio= 0, Bdiff= 1.899e-05, Bkappa=58.99;pos. col. U=21
iter148 errorY= 0.56, prior information ratio= 0, Bdiff= 1.882e-05, Bkappa=59.24;pos. col. U=21
iter149 errorY= 0.56, prior information ratio= 0, Bdiff= 1.865e-05, Bkappa=59.48;pos. col. U=21
iter150 errorY= 0.56, prior information ratio= 0, Bdiff= 1.849e-05, Bkappa=59.72;pos. col. U=21
iter151 errorY= 0.56, prior information ratio= 0, Bdiff= 1.832e-05, Bkappa=59.96;pos. col. U=20
iter152 errorY= 0.56, prior information ratio= 0, Bdiff= 1.816e-05, Bkappa=60.2;pos. col. U=20
iter153 errorY= 0.56, prior information ratio= 0, Bdiff= 1.8e-05, Bkappa=60.43;pos. col. U=20
iter154 errorY= 0.56, prior information ratio= 0, Bdiff= 1.785e-05, Bkappa=60.67;pos. col. U=19
iter155 errorY= 0.56, prior information ratio= 0, Bdiff= 1.77e-05, Bkappa=60.9;pos. col. U=19
iter156 errorY= 0.56, prior information ratio= 0, Bdiff= 1.756e-05, Bkappa=61.14;pos. col. U=19
iter157 errorY= 0.56, prior information ratio= 0, Bdiff= 1.742e-05, Bkappa=61.37;pos. col. U=19
iter158 errorY= 0.56, prior information ratio= 0, Bdiff= 1.729e-05, Bkappa=61.6;pos. col. U=19
iter159 errorY= 0.56, prior information ratio= 0, Bdiff= 1.715e-05, Bkappa=61.83;pos. col. U=19
Updating L3, current fraction= 0.6333, target=0.7
L3 is set to 0.000273 in 4 iterations
iter160 errorY= 0.56, prior information ratio= 0, Bdiff= 1.702e-05, Bkappa=62.06;pos. col. U=22
iter161 errorY= 0.56, prior information ratio= 0, Bdiff= 1.69e-05, Bkappa=62.29;pos. col. U=22
iter162 errorY= 0.56, prior information ratio= 0, Bdiff= 1.678e-05, Bkappa=62.52;pos. col. U=22
iter163 errorY= 0.56, prior information ratio= 0, Bdiff= 1.666e-05, Bkappa=62.75;pos. col. U=22
iter164 errorY= 0.56, prior information ratio= 0, Bdiff= 1.655e-05, Bkappa=62.98;pos. col. U=22
iter165 errorY= 0.56, prior information ratio= 0, Bdiff= 1.643e-05, Bkappa=63.21;pos. col. U=22
iter166 errorY= 0.56, prior information ratio= 0, Bdiff= 1.631e-05, Bkappa=63.43;pos. col. U=22
iter167 errorY= 0.56, prior information ratio= 0, Bdiff= 1.62e-05, Bkappa=63.66;pos. col. U=22
iter168 errorY= 0.56, prior information ratio= 0, Bdiff= 1.609e-05, Bkappa=63.89;pos. col. U=22
iter169 errorY= 0.56, prior information ratio= 0, Bdiff= 1.598e-05, Bkappa=64.11;pos. col. U=22
iter170 errorY= 0.56, prior information ratio= 0, Bdiff= 1.587e-05, Bkappa=64.33;pos. col. U=22
iter171 errorY= 0.56, prior information ratio= 0, Bdiff= 1.576e-05, Bkappa=64.56;pos. col. U=22
iter172 errorY= 0.56, prior information ratio= 0, Bdiff= 1.565e-05, Bkappa=64.78;pos. col. U=22
iter173 errorY= 0.56, prior information ratio= 0, Bdiff= 1.555e-05, Bkappa=65.01;pos. col. U=21
iter174 errorY= 0.56, prior information ratio= 0, Bdiff= 1.545e-05, Bkappa=65.23;pos. col. U=20
iter175 errorY= 0.56, prior information ratio= 0, Bdiff= 1.535e-05, Bkappa=65.45;pos. col. U=20
iter176 errorY= 0.56, prior information ratio= 0, Bdiff= 1.524e-05, Bkappa=65.67;pos. col. U=21
iter177 errorY= 0.56, prior information ratio= 0, Bdiff= 1.514e-05, Bkappa=65.89;pos. col. U=21
iter178 errorY= 0.56, prior information ratio= 0, Bdiff= 1.504e-05, Bkappa=66.12;pos. col. U=21
iter179 errorY= 0.56, prior information ratio= 0, Bdiff= 1.495e-05, Bkappa=66.34;pos. col. U=21
Updating L3, current fraction= 0.7, target=0.7
L3 not changed
iter180 errorY= 0.56, prior information ratio= 0, Bdiff= 1.485e-05, Bkappa=66.56;pos. col. U=21
iter181 errorY= 0.56, prior information ratio= 0, Bdiff= 1.475e-05, Bkappa=66.78;pos. col. U=21
iter182 errorY= 0.56, prior information ratio= 0, Bdiff= 1.466e-05, Bkappa=67;pos. col. U=21
iter183 errorY= 0.56, prior information ratio= 0, Bdiff= 1.456e-05, Bkappa=67.22;pos. col. U=21
iter184 errorY= 0.56, prior information ratio= 0, Bdiff= 1.447e-05, Bkappa=67.44;pos. col. U=21
iter185 errorY= 0.56, prior information ratio= 0, Bdiff= 1.438e-05, Bkappa=67.65;pos. col. U=20
iter186 errorY= 0.56, prior information ratio= 0, Bdiff= 1.429e-05, Bkappa=67.87;pos. col. U=20
iter187 errorY= 0.56, prior information ratio= 0, Bdiff= 1.42e-05, Bkappa=68.09;pos. col. U=20
iter188 errorY= 0.56, prior information ratio= 0, Bdiff= 1.411e-05, Bkappa=68.31;pos. col. U=20
iter189 errorY= 0.56, prior information ratio= 0, Bdiff= 1.402e-05, Bkappa=68.52;pos. col. U=20
iter190 errorY= 0.56, prior information ratio= 0, Bdiff= 1.393e-05, Bkappa=68.74;pos. col. U=20
iter191 errorY= 0.56, prior information ratio= 0, Bdiff= 1.384e-05, Bkappa=68.96;pos. col. U=20
iter192 errorY= 0.56, prior information ratio= 0, Bdiff= 1.376e-05, Bkappa=69.17;pos. col. U=20
iter193 errorY= 0.56, prior information ratio= 0, Bdiff= 1.368e-05, Bkappa=69.39;pos. col. U=19
iter194 errorY= 0.56, prior information ratio= 0, Bdiff= 1.36e-05, Bkappa=69.6;pos. col. U=19
iter195 errorY= 0.56, prior information ratio= 0, Bdiff= 1.353e-05, Bkappa=69.82;pos. col. U=19
iter196 errorY= 0.56, prior information ratio= 0, Bdiff= 1.345e-05, Bkappa=70.03;pos. col. U=19
iter197 errorY= 0.56, prior information ratio= 0, Bdiff= 1.338e-05, Bkappa=70.25;pos. col. U=19
iter198 errorY= 0.56, prior information ratio= 0, Bdiff= 1.331e-05, Bkappa=70.46;pos. col. U=19
iter199 errorY= 0.56, prior information ratio= 0, Bdiff= 1.325e-05, Bkappa=70.68;pos. col. U=19
Updating L3, current fraction= 0.6333, target=0.7
L3 is set to 0.000256 in 4 iterations
iter200 errorY= 0.56, prior information ratio= 0, Bdiff= 1.318e-05, Bkappa=70.9;pos. col. U=22
iter201 errorY= 0.56, prior information ratio= 0, Bdiff= 1.312e-05, Bkappa=71.11;pos. col. U=21
iter202 errorY= 0.56, prior information ratio= 0, Bdiff= 1.306e-05, Bkappa=71.33;pos. col. U=21
iter203 errorY= 0.56, prior information ratio= 0, Bdiff= 1.3e-05, Bkappa=71.55;pos. col. U=21
iter204 errorY= 0.56, prior information ratio= 0, Bdiff= 1.294e-05, Bkappa=71.76;pos. col. U=21
iter205 errorY= 0.56, prior information ratio= 0, Bdiff= 1.288e-05, Bkappa=71.98;pos. col. U=21
iter206 errorY= 0.56, prior information ratio= 0, Bdiff= 1.282e-05, Bkappa=72.2;pos. col. U=21
iter207 errorY= 0.56, prior information ratio= 0, Bdiff= 1.276e-05, Bkappa=72.42;pos. col. U=21
iter208 errorY= 0.56, prior information ratio= 0, Bdiff= 1.271e-05, Bkappa=72.63;pos. col. U=21
iter209 errorY= 0.56, prior information ratio= 0, Bdiff= 1.265e-05, Bkappa=72.85;pos. col. U=21
iter210 errorY= 0.56, prior information ratio= 0, Bdiff= 1.259e-05, Bkappa=73.07;pos. col. U=21
iter211 errorY= 0.56, prior information ratio= 0, Bdiff= 1.253e-05, Bkappa=73.29;pos. col. U=21
iter212 errorY= 0.56, prior information ratio= 0, Bdiff= 1.248e-05, Bkappa=73.5;pos. col. U=21
iter213 errorY= 0.56, prior information ratio= 0, Bdiff= 1.242e-05, Bkappa=73.72;pos. col. U=21
iter214 errorY= 0.56, prior information ratio= 0, Bdiff= 1.237e-05, Bkappa=73.94;pos. col. U=21
iter215 errorY= 0.56, prior information ratio= 0, Bdiff= 1.231e-05, Bkappa=74.16;pos. col. U=21
iter216 errorY= 0.56, prior information ratio= 0, Bdiff= 1.226e-05, Bkappa=74.38;pos. col. U=21
iter217 errorY= 0.56, prior information ratio= 0, Bdiff= 1.221e-05, Bkappa=74.59;pos. col. U=21
iter218 errorY= 0.56, prior information ratio= 0, Bdiff= 1.215e-05, Bkappa=74.81;pos. col. U=21
iter219 errorY= 0.56, prior information ratio= 0, Bdiff= 1.21e-05, Bkappa=75.03;pos. col. U=21
Updating L3, current fraction= 0.7, target=0.7
L3 not changed
iter220 errorY= 0.56, prior information ratio= 0, Bdiff= 1.205e-05, Bkappa=75.25;pos. col. U=20
iter221 errorY= 0.56, prior information ratio= 0, Bdiff= 1.2e-05, Bkappa=75.47;pos. col. U=20
iter222 errorY= 0.56, prior information ratio= 0, Bdiff= 1.194e-05, Bkappa=75.68;pos. col. U=20
iter223 errorY= 0.56, prior information ratio= 0, Bdiff= 1.189e-05, Bkappa=75.9;pos. col. U=20
iter224 errorY= 0.56, prior information ratio= 0, Bdiff= 1.183e-05, Bkappa=76.12;pos. col. U=20
iter225 errorY= 0.56, prior information ratio= 0, Bdiff= 1.179e-05, Bkappa=76.33;pos. col. U=20
iter226 errorY= 0.56, prior information ratio= 0, Bdiff= 1.174e-05, Bkappa=76.55;pos. col. U=20
iter227 errorY= 0.56, prior information ratio= 0, Bdiff= 1.17e-05, Bkappa=76.77;pos. col. U=20
iter228 errorY= 0.56, prior information ratio= 0, Bdiff= 1.166e-05, Bkappa=76.99;pos. col. U=20
iter229 errorY= 0.56, prior information ratio= 0, Bdiff= 1.161e-05, Bkappa=77.21;pos. col. U=20
iter230 errorY= 0.56, prior information ratio= 0, Bdiff= 1.157e-05, Bkappa=77.43;pos. col. U=20
iter231 errorY= 0.56, prior information ratio= 0, Bdiff= 1.153e-05, Bkappa=77.64;pos. col. U=20
iter232 errorY= 0.56, prior information ratio= 0, Bdiff= 1.149e-05, Bkappa=77.86;pos. col. U=20
iter233 errorY= 0.56, prior information ratio= 0, Bdiff= 1.145e-05, Bkappa=78.08;pos. col. U=20
iter234 errorY= 0.56, prior information ratio= 0, Bdiff= 1.141e-05, Bkappa=78.3;pos. col. U=20
iter235 errorY= 0.56, prior information ratio= 0, Bdiff= 1.137e-05, Bkappa=78.51;pos. col. U=20
iter236 errorY= 0.56, prior information ratio= 0, Bdiff= 1.133e-05, Bkappa=78.73;pos. col. U=20
iter237 errorY= 0.56, prior information ratio= 0, Bdiff= 1.129e-05, Bkappa=78.94;pos. col. U=20
iter238 errorY= 0.56, prior information ratio= 0, Bdiff= 1.125e-05, Bkappa=79.15;pos. col. U=20
iter239 errorY= 0.56, prior information ratio= 0, Bdiff= 1.121e-05, Bkappa=79.37;pos. col. U=20
Updating L3, current fraction= 0.6667, target=0.7
L3 not changed
iter240 errorY= 0.56, prior information ratio= 0, Bdiff= 1.117e-05, Bkappa=79.58;pos. col. U=20
iter241 errorY= 0.56, prior information ratio= 0, Bdiff= 1.113e-05, Bkappa=79.8;pos. col. U=20
iter242 errorY= 0.56, prior information ratio= 0, Bdiff= 1.109e-05, Bkappa=80.01;pos. col. U=20
iter243 errorY= 0.56, prior information ratio= 0, Bdiff= 1.105e-05, Bkappa=80.22;pos. col. U=20
iter244 errorY= 0.56, prior information ratio= 0, Bdiff= 1.102e-05, Bkappa=80.44;pos. col. U=20
iter245 errorY= 0.56, prior information ratio= 0, Bdiff= 1.098e-05, Bkappa=80.65;pos. col. U=20
iter246 errorY= 0.56, prior information ratio= 0, Bdiff= 1.095e-05, Bkappa=80.86;pos. col. U=20
iter247 errorY= 0.56, prior information ratio= 0, Bdiff= 1.091e-05, Bkappa=81.08;pos. col. U=20
iter248 errorY= 0.56, prior information ratio= 0, Bdiff= 1.088e-05, Bkappa=81.29;pos. col. U=19
iter249 errorY= 0.56, prior information ratio= 0, Bdiff= 1.085e-05, Bkappa=81.51;pos. col. U=19
iter250 errorY= 0.56, prior information ratio= 0, Bdiff= 1.082e-05, Bkappa=81.72;pos. col. U=19
iter251 errorY= 0.56, prior information ratio= 0, Bdiff= 1.08e-05, Bkappa=81.93;pos. col. U=19
iter252 errorY= 0.56, prior information ratio= 0, Bdiff= 1.077e-05, Bkappa=82.15;pos. col. U=19
iter253 errorY= 0.56, prior information ratio= 0, Bdiff= 1.074e-05, Bkappa=82.36;pos. col. U=19
iter254 errorY= 0.56, prior information ratio= 0, Bdiff= 1.072e-05, Bkappa=82.57;pos. col. U=19
iter255 errorY= 0.56, prior information ratio= 0, Bdiff= 1.069e-05, Bkappa=82.79;pos. col. U=18
iter256 errorY= 0.56, prior information ratio= 0, Bdiff= 1.067e-05, Bkappa=83;pos. col. U=18
iter257 errorY= 0.56, prior information ratio= 0, Bdiff= 1.064e-05, Bkappa=83.22;pos. col. U=18
iter258 errorY= 0.56, prior information ratio= 0, Bdiff= 1.062e-05, Bkappa=83.43;pos. col. U=18
iter259 errorY= 0.56, prior information ratio= 0, Bdiff= 1.059e-05, Bkappa=83.64;pos. col. U=18
Updating L3, current fraction= 0.6, target=0.7
L3 is set to 0.000224 in 3 iterations
iter260 errorY= 0.56, prior information ratio= 0, Bdiff= 1.057e-05, Bkappa=83.86;pos. col. U=22
iter261 errorY= 0.56, prior information ratio= 0, Bdiff= 1.054e-05, Bkappa=84.07;pos. col. U=22
iter262 errorY= 0.56, prior information ratio= 0, Bdiff= 1.052e-05, Bkappa=84.28;pos. col. U=21
iter263 errorY= 0.56, prior information ratio= 0, Bdiff= 1.05e-05, Bkappa=84.49;pos. col. U=21
iter264 errorY= 0.56, prior information ratio= 0, Bdiff= 1.047e-05, Bkappa=84.71;pos. col. U=21
iter265 errorY= 0.56, prior information ratio= 0, Bdiff= 1.045e-05, Bkappa=84.92;pos. col. U=21
iter266 errorY= 0.56, prior information ratio= 0, Bdiff= 1.043e-05, Bkappa=85.13;pos. col. U=21
iter267 errorY= 0.56, prior information ratio= 0, Bdiff= 1.041e-05, Bkappa=85.34;pos. col. U=21
iter268 errorY= 0.56, prior information ratio= 0, Bdiff= 1.039e-05, Bkappa=85.55;pos. col. U=21
iter269 errorY= 0.56, prior information ratio= 0, Bdiff= 1.037e-05, Bkappa=85.77;pos. col. U=21
iter270 errorY= 0.56, prior information ratio= 0, Bdiff= 1.034e-05, Bkappa=85.98;pos. col. U=21
iter271 errorY= 0.56, prior information ratio= 0, Bdiff= 1.033e-05, Bkappa=86.19;pos. col. U=21
iter272 errorY= 0.56, prior information ratio= 0, Bdiff= 1.031e-05, Bkappa=86.4;pos. col. U=21
iter273 errorY= 0.56, prior information ratio= 0, Bdiff= 1.029e-05, Bkappa=86.61;pos. col. U=21
iter274 errorY= 0.56, prior information ratio= 0, Bdiff= 1.027e-05, Bkappa=86.82;pos. col. U=21
iter275 errorY= 0.56, prior information ratio= 0, Bdiff= 1.025e-05, Bkappa=87.03;pos. col. U=21
iter276 errorY= 0.56, prior information ratio= 0, Bdiff= 1.023e-05, Bkappa=87.24;pos. col. U=21
iter277 errorY= 0.56, prior information ratio= 0, Bdiff= 1.022e-05, Bkappa=87.45;pos. col. U=21
iter278 errorY= 0.56, prior information ratio= 0, Bdiff= 1.02e-05, Bkappa=87.66;pos. col. U=21
iter279 errorY= 0.56, prior information ratio= 0, Bdiff= 1.018e-05, Bkappa=87.87;pos. col. U=21
Updating L3, current fraction= 0.7, target=0.7
L3 not changed
iter280 errorY= 0.56, prior information ratio= 0, Bdiff= 1.017e-05, Bkappa=88.08;pos. col. U=20
iter281 errorY= 0.56, prior information ratio= 0, Bdiff= 1.015e-05, Bkappa=88.29;pos. col. U=20
iter282 errorY= 0.56, prior information ratio= 0, Bdiff= 1.014e-05, Bkappa=88.5;pos. col. U=20
iter283 errorY= 0.56, prior information ratio= 0, Bdiff= 1.012e-05, Bkappa=88.71;pos. col. U=20
iter284 errorY= 0.56, prior information ratio= 0, Bdiff= 1.011e-05, Bkappa=88.92;pos. col. U=20
iter285 errorY= 0.56, prior information ratio= 0, Bdiff= 1.01e-05, Bkappa=89.13;pos. col. U=20
iter286 errorY= 0.56, prior information ratio= 0, Bdiff= 1.009e-05, Bkappa=89.34;pos. col. U=20
iter287 errorY= 0.56, prior information ratio= 0, Bdiff= 1.008e-05, Bkappa=89.55;pos. col. U=20
iter288 errorY= 0.56, prior information ratio= 0, Bdiff= 1.007e-05, Bkappa=89.76;pos. col. U=20
iter289 errorY= 0.56, prior information ratio= 0, Bdiff= 1.006e-05, Bkappa=89.97;pos. col. U=20
iter290 errorY= 0.56, prior information ratio= 0, Bdiff= 1.006e-05, Bkappa=90.18;pos. col. U=20
iter291 errorY= 0.56, prior information ratio= 0, Bdiff= 1.005e-05, Bkappa=90.39;pos. col. U=20
iter292 errorY= 0.56, prior information ratio= 0, Bdiff= 1.004e-05, Bkappa=90.6;pos. col. U=20
iter293 errorY= 0.56, prior information ratio= 0, Bdiff= 1.004e-05, Bkappa=90.81;pos. col. U=20
iter294 errorY= 0.56, prior information ratio= 0, Bdiff= 1.003e-05, Bkappa=91.02;pos. col. U=20
iter295 errorY= 0.56, prior information ratio= 0, Bdiff= 1.003e-05, Bkappa=91.23;pos. col. U=20
iter296 errorY= 0.56, prior information ratio= 0, Bdiff= 1.003e-05, Bkappa=91.44;pos. col. U=20
iter297 errorY= 0.56, prior information ratio= 0, Bdiff= 1.003e-05, Bkappa=91.65;pos. col. U=20
iter298 errorY= 0.56, prior information ratio= 0, Bdiff= 1.003e-05, Bkappa=91.86;pos. col. U=20
iter299 errorY= 0.56, prior information ratio= 0, Bdiff= 1.003e-05, Bkappa=92.07;pos. col. U=20
Updating L3, current fraction= 0.6667, target=0.7
L3 not changed
iter300 errorY= 0.56, prior information ratio= 0, Bdiff= 1.003e-05, Bkappa=92.28;pos. col. U=20
iter301 errorY= 0.56, prior information ratio= 0, Bdiff= 1.003e-05, Bkappa=91.72;pos. col. U=20
iter302 errorY= 0.56, prior information ratio= 0, Bdiff= 1.003e-05, Bkappa=91.93;pos. col. U=20
iter303 errorY= 0.56, prior information ratio= 0, Bdiff= 1.003e-05, Bkappa=92.14;pos. col. U=20
iter304 errorY= 0.56, prior information ratio= 0, Bdiff= 1.003e-05, Bkappa=92.36;pos. col. U=20
iter305 errorY= 0.56, prior information ratio= 0, Bdiff= 1.004e-05, Bkappa=92.57;pos. col. U=20
iter306 errorY= 0.56, prior information ratio= 0, Bdiff= 1.005e-05, Bkappa=92.78;pos. col. U=20
iter307 errorY= 0.56, prior information ratio= 0, Bdiff= 1.006e-05, Bkappa=92.99;pos. col. U=20
iter308 errorY= 0.56, prior information ratio= 0, Bdiff= 1.007e-05, Bkappa=93.21;pos. col. U=20
iter309 errorY= 0.56, prior information ratio= 0, Bdiff= 1.008e-05, Bkappa=93.42;pos. col. U=20
iter310 errorY= 0.56, prior information ratio= 0, Bdiff= 1.01e-05, Bkappa=93.63;pos. col. U=20
iter311 errorY= 0.56, prior information ratio= 0, Bdiff= 1.011e-05, Bkappa=93.84;pos. col. U=20
iter312 errorY= 0.56, prior information ratio= 0, Bdiff= 1.013e-05, Bkappa=94.05;pos. col. U=20
iter313 errorY= 0.56, prior information ratio= 0, Bdiff= 1.014e-05, Bkappa=94.27;pos. col. U=20
iter314 errorY= 0.56, prior information ratio= 0, Bdiff= 1.016e-05, Bkappa=94.48;pos. col. U=20
iter315 errorY= 0.56, prior information ratio= 0, Bdiff= 1.018e-05, Bkappa=94.69;pos. col. U=20
iter316 errorY= 0.56, prior information ratio= 0, Bdiff= 1.019e-05, Bkappa=94.9;pos. col. U=20
iter317 errorY= 0.56, prior information ratio= 0, Bdiff= 1.021e-05, Bkappa=95.12;pos. col. U=20
iter318 errorY= 0.56, prior information ratio= 0, Bdiff= 1.023e-05, Bkappa=95.33;pos. col. U=20
iter319 errorY= 0.56, prior information ratio= 0, Bdiff= 1.025e-05, Bkappa=95.54;pos. col. U=20
Updating L3, current fraction= 0.6667, target=0.7
L3 not changed
iter320 errorY= 0.56, prior information ratio= 0, Bdiff= 1.027e-05, Bkappa=95.75;pos. col. U=20
iter321 errorY= 0.56, prior information ratio= 0, Bdiff= 1.029e-05, Bkappa=95.97;pos. col. U=20
iter322 errorY= 0.56, prior information ratio= 0, Bdiff= 1.032e-05, Bkappa=96.18;pos. col. U=20
Bdiff is not decreasing
iter323 errorY= 0.56, prior information ratio= 0, Bdiff= 1.034e-05, Bkappa=96.39;pos. col. U=20
Bdiff is not decreasing
iter324 errorY= 0.56, prior information ratio= 0, Bdiff= 1.037e-05, Bkappa=96.61;pos. col. U=20
Bdiff is not decreasing
iter325 errorY= 0.56, prior information ratio= 0, Bdiff= 1.04e-05, Bkappa=96.82;pos. col. U=20
Bdiff is not decreasing
iter326 errorY= 0.56, prior information ratio= 0, Bdiff= 1.042e-05, Bkappa=97.03;pos. col. U=20
Bdiff is not decreasing
iter327 errorY= 0.56, prior information ratio= 0, Bdiff= 1.046e-05, Bkappa=97.25;pos. col. U=20
Bdiff is not decreasing
converged at  iteration 327 Bdiff is not decreasing
There are 15  LVs with AUC>0.70



Removing 1 pathways with too few genesComputing SVD
Done
errorY (SVD based:best possible) = 0.5578
iter1 errorY= 0.6576, Bdiff= 0.4849, Bkappa=27.15
iter2 errorY= 0.599, Bdiff= 0.1143, Bkappa=44.12
iter3 errorY= 0.584, Bdiff= 0.03907, Bkappa=57.09
iter4 errorY= 0.5778, Bdiff= 0.01811, Bkappa=67.11
iter5 errorY= 0.5744, Bdiff= 0.009848, Bkappa=74.98
iter6 errorY= 0.5724, Bdiff= 0.006188, Bkappa=81.44
iter7 errorY= 0.5709, Bdiff= 0.004327, Bkappa=88.93
iter8 errorY= 0.5698, Bdiff= 0.003266, Bkappa=93.99
iter9 errorY= 0.569, Bdiff= 0.002619, Bkappa=98.57
iter10 errorY= 0.5683, Bdiff= 0.002165, Bkappa=102.8
iter11 errorY= 0.5677, Bdiff= 0.001844, Bkappa=106.7
iter12 errorY= 0.5672, Bdiff= 0.001618, Bkappa=110.4
iter13 errorY= 0.5668, Bdiff= 0.001454, Bkappa=114
iter14 errorY= 0.5664, Bdiff= 0.001327, Bkappa=115.7
iter15 errorY= 0.566, Bdiff= 0.00121, Bkappa=118.9
iter16 errorY= 0.5657, Bdiff= 0.001092, Bkappa=121.9
iter17 errorY= 0.5654, Bdiff= 0.0009703, Bkappa=124.8
iter18 errorY= 0.5651, Bdiff= 0.0008504, Bkappa=127.4
iter19 errorY= 0.5649, Bdiff= 0.0007422, Bkappa=129.7
Updating L3, current fraction= 0, target=0.7
L3 is set to 0.000451 in 17 iterations
iter20 errorY= 0.5647, prior information ratio= 0, Bdiff= 0.00065, Bkappa=131.9;pos. col. U=18
iter21 errorY= 0.5645, prior information ratio= 0, Bdiff= 0.0005686, Bkappa=133.9;pos. col. U=19
iter22 errorY= 0.5643, prior information ratio= 0, Bdiff= 0.000495, Bkappa=135.7;pos. col. U=20
iter23 errorY= 0.5641, prior information ratio= 0, Bdiff= 0.0004329, Bkappa=137.2;pos. col. U=20
iter24 errorY= 0.564, prior information ratio= 0, Bdiff= 0.0003818, Bkappa=138.6;pos. col. U=20
iter25 errorY= 0.5638, prior information ratio= 0, Bdiff= 0.0003393, Bkappa=139.9;pos. col. U=20
iter26 errorY= 0.5637, prior information ratio= 0, Bdiff= 0.000305, Bkappa=141;pos. col. U=20
iter27 errorY= 0.5636, prior information ratio= 0, Bdiff= 0.0002775, Bkappa=142;pos. col. U=20
iter28 errorY= 0.5634, prior information ratio= 0, Bdiff= 0.0002542, Bkappa=142.9;pos. col. U=20
iter29 errorY= 0.5633, prior information ratio= 0, Bdiff= 0.0002339, Bkappa=143.7;pos. col. U=20
iter30 errorY= 0.5632, prior information ratio= 0, Bdiff= 0.0002159, Bkappa=144.5;pos. col. U=20
iter31 errorY= 0.5631, prior information ratio= 0, Bdiff= 0.0001999, Bkappa=145.2;pos. col. U=20
iter32 errorY= 0.563, prior information ratio= 0, Bdiff= 0.0001866, Bkappa=145.8;pos. col. U=20
iter33 errorY= 0.5629, prior information ratio= 0, Bdiff= 0.0001753, Bkappa=146.4;pos. col. U=20
iter34 errorY= 0.5629, prior information ratio= 0, Bdiff= 0.0001647, Bkappa=146.9;pos. col. U=20
iter35 errorY= 0.5628, prior information ratio= 0, Bdiff= 0.0001553, Bkappa=147.4;pos. col. U=20
iter36 errorY= 0.5627, prior information ratio= 0, Bdiff= 0.0001472, Bkappa=147.9;pos. col. U=20
iter37 errorY= 0.5626, prior information ratio= 0, Bdiff= 0.0001408, Bkappa=148.4;pos. col. U=21
iter38 errorY= 0.5626, prior information ratio= 0, Bdiff= 0.0001348, Bkappa=148.8;pos. col. U=20
iter39 errorY= 0.5625, prior information ratio= 0, Bdiff= 0.0001296, Bkappa=149.2;pos. col. U=20
Updating L3, current fraction= 0.7407, target=0.7
L3 is set to 0.000495 in 10 iterations
iter40 errorY= 0.5625, prior information ratio= 0, Bdiff= 0.000125, Bkappa=149.6;pos. col. U=18
iter41 errorY= 0.5624, prior information ratio= 0, Bdiff= 0.0001202, Bkappa=150;pos. col. U=18
iter42 errorY= 0.5624, prior information ratio= 0, Bdiff= 0.0001155, Bkappa=150.3;pos. col. U=18
iter43 errorY= 0.5623, prior information ratio= 0, Bdiff= 0.0001113, Bkappa=150.7;pos. col. U=18
iter44 errorY= 0.5623, prior information ratio= 0, Bdiff= 0.0001078, Bkappa=149;pos. col. U=18
iter45 errorY= 0.5622, prior information ratio= 0, Bdiff= 0.0001042, Bkappa=149.5;pos. col. U=18
iter46 errorY= 0.5622, prior information ratio= 0, Bdiff= 0.0001009, Bkappa=149.8;pos. col. U=18
iter47 errorY= 0.5621, prior information ratio= 0, Bdiff= 9.825e-05, Bkappa=150.1;pos. col. U=18
iter48 errorY= 0.5621, prior information ratio= 0, Bdiff= 9.63e-05, Bkappa=150.4;pos. col. U=17
iter49 errorY= 0.5621, prior information ratio= 0, Bdiff= 9.499e-05, Bkappa=150.6;pos. col. U=17
iter50 errorY= 0.562, prior information ratio= 0, Bdiff= 9.416e-05, Bkappa=150.8;pos. col. U=17
iter51 errorY= 0.562, prior information ratio= 0, Bdiff= 9.366e-05, Bkappa=150.9;pos. col. U=17
iter52 errorY= 0.562, prior information ratio= 0, Bdiff= 9.351e-05, Bkappa=150.3;pos. col. U=17
iter53 errorY= 0.562, prior information ratio= 0, Bdiff= 9.316e-05, Bkappa=150.3;pos. col. U=17
iter54 errorY= 0.5619, prior information ratio= 0, Bdiff= 9.014e-05, Bkappa=150.4;pos. col. U=17
iter55 errorY= 0.5619, prior information ratio= 0, Bdiff= 8.587e-05, Bkappa=151.5;pos. col. U=17
iter56 errorY= 0.5619, prior information ratio= 0, Bdiff= 8.499e-05, Bkappa=151.7;pos. col. U=17
iter57 errorY= 0.5618, prior information ratio= 0, Bdiff= 8.739e-05, Bkappa=152;pos. col. U=17
iter58 errorY= 0.5618, prior information ratio= 0, Bdiff= 9.176e-05, Bkappa=152.4;pos. col. U=17
iter59 errorY= 0.5618, prior information ratio= 0, Bdiff= 9.441e-05, Bkappa=152.8;pos. col. U=16
Updating L3, current fraction= 0.5926, target=0.7
L3 is set to 0.000434 in 3 iterations
iter60 errorY= 0.5617, prior information ratio= 0, Bdiff= 9.495e-05, Bkappa=153.2;pos. col. U=19
iter61 errorY= 0.5617, prior information ratio= 0, Bdiff= 9.499e-05, Bkappa=153.7;pos. col. U=18
iter62 errorY= 0.5617, prior information ratio= 0, Bdiff= 9.353e-05, Bkappa=154.2;pos. col. U=18
iter63 errorY= 0.5616, prior information ratio= 0, Bdiff= 8.942e-05, Bkappa=154.6;pos. col. U=18
iter64 errorY= 0.5616, prior information ratio= 0, Bdiff= 8.406e-05, Bkappa=155.1;pos. col. U=18
iter65 errorY= 0.5616, prior information ratio= 0, Bdiff= 8e-05, Bkappa=155.5;pos. col. U=18
iter66 errorY= 0.5616, prior information ratio= 0, Bdiff= 7.679e-05, Bkappa=155.9;pos. col. U=18
iter67 errorY= 0.5615, prior information ratio= 0, Bdiff= 7.446e-05, Bkappa=156.4;pos. col. U=18
iter68 errorY= 0.5615, prior information ratio= 0, Bdiff= 7.264e-05, Bkappa=156.8;pos. col. U=18
iter69 errorY= 0.5615, prior information ratio= 0, Bdiff= 7.098e-05, Bkappa=157.3;pos. col. U=18
iter70 errorY= 0.5615, prior information ratio= 0, Bdiff= 6.952e-05, Bkappa=157.7;pos. col. U=18
iter71 errorY= 0.5615, prior information ratio= 0, Bdiff= 6.829e-05, Bkappa=158.1;pos. col. U=18
iter72 errorY= 0.5614, prior information ratio= 0, Bdiff= 6.725e-05, Bkappa=158.6;pos. col. U=18
iter73 errorY= 0.5614, prior information ratio= 0, Bdiff= 6.631e-05, Bkappa=159;pos. col. U=18
iter74 errorY= 0.5614, prior information ratio= 0, Bdiff= 6.544e-05, Bkappa=159.5;pos. col. U=18
iter75 errorY= 0.5614, prior information ratio= 0, Bdiff= 6.466e-05, Bkappa=159.9;pos. col. U=18
iter76 errorY= 0.5614, prior information ratio= 0, Bdiff= 6.391e-05, Bkappa=160.4;pos. col. U=18
iter77 errorY= 0.5614, prior information ratio= 0, Bdiff= 6.33e-05, Bkappa=160.9;pos. col. U=18
iter78 errorY= 0.5613, prior information ratio= 0, Bdiff= 6.273e-05, Bkappa=161.3;pos. col. U=18
iter79 errorY= 0.5613, prior information ratio= 0, Bdiff= 6.221e-05, Bkappa=161.8;pos. col. U=18
Updating L3, current fraction= 0.6667, target=0.7
L3 not changed
iter80 errorY= 0.5613, prior information ratio= 0, Bdiff= 6.171e-05, Bkappa=162.3;pos. col. U=18
iter81 errorY= 0.5613, prior information ratio= 0, Bdiff= 6.124e-05, Bkappa=162.8;pos. col. U=18
iter82 errorY= 0.5613, prior information ratio= 0, Bdiff= 6.076e-05, Bkappa=163.2;pos. col. U=17
iter83 errorY= 0.5613, prior information ratio= 0, Bdiff= 6.034e-05, Bkappa=163.7;pos. col. U=17
iter84 errorY= 0.5613, prior information ratio= 0, Bdiff= 5.991e-05, Bkappa=164.2;pos. col. U=17
iter85 errorY= 0.5613, prior information ratio= 0, Bdiff= 5.951e-05, Bkappa=164.7;pos. col. U=17
iter86 errorY= 0.5612, prior information ratio= 0, Bdiff= 5.909e-05, Bkappa=165.2;pos. col. U=17
iter87 errorY= 0.5612, prior information ratio= 0, Bdiff= 5.866e-05, Bkappa=165.7;pos. col. U=17
iter88 errorY= 0.5612, prior information ratio= 0, Bdiff= 5.834e-05, Bkappa=62.42;pos. col. U=17
iter89 errorY= 0.5612, prior information ratio= 0, Bdiff= 5.804e-05, Bkappa=62.61;pos. col. U=17
iter90 errorY= 0.5612, prior information ratio= 0, Bdiff= 5.775e-05, Bkappa=62.8;pos. col. U=16
iter91 errorY= 0.5612, prior information ratio= 0, Bdiff= 5.747e-05, Bkappa=63;pos. col. U=16
iter92 errorY= 0.5612, prior information ratio= 0, Bdiff= 5.717e-05, Bkappa=63.19;pos. col. U=16
iter93 errorY= 0.5612, prior information ratio= 0, Bdiff= 5.679e-05, Bkappa=63.39;pos. col. U=16
iter94 errorY= 0.5612, prior information ratio= 0, Bdiff= 5.64e-05, Bkappa=63.59;pos. col. U=16
iter95 errorY= 0.5611, prior information ratio= 0, Bdiff= 5.601e-05, Bkappa=63.79;pos. col. U=16
iter96 errorY= 0.5611, prior information ratio= 0, Bdiff= 5.562e-05, Bkappa=64;pos. col. U=16
iter97 errorY= 0.5611, prior information ratio= 0, Bdiff= 5.518e-05, Bkappa=64.2;pos. col. U=16
iter98 errorY= 0.5611, prior information ratio= 0, Bdiff= 5.469e-05, Bkappa=64.4;pos. col. U=16
iter99 errorY= 0.5611, prior information ratio= 0, Bdiff= 5.42e-05, Bkappa=64.61;pos. col. U=16
Updating L3, current fraction= 0.5926, target=0.7
L3 is set to 0.00038 in 3 iterations
iter100 errorY= 0.5611, prior information ratio= 0, Bdiff= 5.371e-05, Bkappa=64.81;pos. col. U=18
iter101 errorY= 0.5611, prior information ratio= 0, Bdiff= 5.327e-05, Bkappa=65.02;pos. col. U=18
iter102 errorY= 0.5611, prior information ratio= 0, Bdiff= 5.282e-05, Bkappa=65.22;pos. col. U=18
iter103 errorY= 0.5611, prior information ratio= 0, Bdiff= 5.234e-05, Bkappa=65.43;pos. col. U=18
iter104 errorY= 0.5611, prior information ratio= 0, Bdiff= 5.185e-05, Bkappa=65.64;pos. col. U=18
iter105 errorY= 0.5611, prior information ratio= 0, Bdiff= 5.138e-05, Bkappa=65.84;pos. col. U=18
iter106 errorY= 0.561, prior information ratio= 0, Bdiff= 5.095e-05, Bkappa=66.05;pos. col. U=18
iter107 errorY= 0.561, prior information ratio= 0, Bdiff= 5.055e-05, Bkappa=66.25;pos. col. U=18
iter108 errorY= 0.561, prior information ratio= 0, Bdiff= 5.017e-05, Bkappa=66.46;pos. col. U=17
iter109 errorY= 0.561, prior information ratio= 0, Bdiff= 4.981e-05, Bkappa=66.66;pos. col. U=17
iter110 errorY= 0.561, prior information ratio= 0, Bdiff= 4.949e-05, Bkappa=66.88;pos. col. U=17
iter111 errorY= 0.561, prior information ratio= 0, Bdiff= 4.918e-05, Bkappa=67.11;pos. col. U=17
iter112 errorY= 0.561, prior information ratio= 0, Bdiff= 4.888e-05, Bkappa=67.33;pos. col. U=17
iter113 errorY= 0.561, prior information ratio= 0, Bdiff= 4.859e-05, Bkappa=67.56;pos. col. U=17
iter114 errorY= 0.561, prior information ratio= 0, Bdiff= 4.831e-05, Bkappa=67.79;pos. col. U=17
iter115 errorY= 0.561, prior information ratio= 0, Bdiff= 4.807e-05, Bkappa=68.01;pos. col. U=17
iter116 errorY= 0.561, prior information ratio= 0, Bdiff= 4.782e-05, Bkappa=68.24;pos. col. U=17
iter117 errorY= 0.561, prior information ratio= 0, Bdiff= 4.758e-05, Bkappa=68.47;pos. col. U=17
iter118 errorY= 0.561, prior information ratio= 0, Bdiff= 4.731e-05, Bkappa=68.7;pos. col. U=17
iter119 errorY= 0.561, prior information ratio= 0, Bdiff= 4.702e-05, Bkappa=68.93;pos. col. U=17
Updating L3, current fraction= 0.6296, target=0.7
L3 is set to 0.000356 in 4 iterations
iter120 errorY= 0.561, prior information ratio= 0, Bdiff= 4.674e-05, Bkappa=69.16;pos. col. U=18
iter121 errorY= 0.561, prior information ratio= 0, Bdiff= 4.646e-05, Bkappa=69.39;pos. col. U=18
iter122 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.618e-05, Bkappa=87.92;pos. col. U=18
iter123 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.589e-05, Bkappa=88.18;pos. col. U=18
iter124 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.568e-05, Bkappa=88.44;pos. col. U=18
iter125 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.551e-05, Bkappa=88.7;pos. col. U=18
iter126 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.535e-05, Bkappa=88.96;pos. col. U=18
iter127 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.522e-05, Bkappa=89.23;pos. col. U=18
iter128 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.514e-05, Bkappa=89.49;pos. col. U=18
iter129 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.512e-05, Bkappa=89.76;pos. col. U=18
iter130 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.514e-05, Bkappa=90.03;pos. col. U=18
iter131 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.516e-05, Bkappa=90.3;pos. col. U=17
iter132 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.519e-05, Bkappa=90.57;pos. col. U=17
iter133 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.522e-05, Bkappa=90.84;pos. col. U=17
iter134 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.529e-05, Bkappa=118.9;pos. col. U=17
iter135 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.536e-05, Bkappa=119.2;pos. col. U=17
iter136 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.543e-05, Bkappa=119.5;pos. col. U=17
iter137 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.554e-05, Bkappa=119.9;pos. col. U=17
iter138 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.565e-05, Bkappa=120.2;pos. col. U=17
iter139 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.578e-05, Bkappa=120.5;pos. col. U=17
Updating L3, current fraction= 0.6296, target=0.7
L3 is set to 0.000332 in 7 iterations
iter140 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.589e-05, Bkappa=120.8;pos. col. U=19
iter141 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.599e-05, Bkappa=121.2;pos. col. U=17
iter142 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.614e-05, Bkappa=121.5;pos. col. U=17
iter143 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.633e-05, Bkappa=121.8;pos. col. U=17
iter144 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.655e-05, Bkappa=122.2;pos. col. U=17
iter145 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.676e-05, Bkappa=122.5;pos. col. U=17
iter146 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.699e-05, Bkappa=122.9;pos. col. U=16
iter147 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.725e-05, Bkappa=166.4;pos. col. U=16
iter148 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.752e-05, Bkappa=166.8;pos. col. U=16
iter149 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.779e-05, Bkappa=167.3;pos. col. U=16
iter150 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.806e-05, Bkappa=167.7;pos. col. U=16
iter151 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.833e-05, Bkappa=168.2;pos. col. U=16
iter152 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.86e-05, Bkappa=168.6;pos. col. U=16
iter153 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.884e-05, Bkappa=169.1;pos. col. U=16
iter154 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.905e-05, Bkappa=169.5;pos. col. U=16
iter155 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.925e-05, Bkappa=170;pos. col. U=16
iter156 errorY= 0.5609, prior information ratio= 0, Bdiff= 4.947e-05, Bkappa=170.4;pos. col. U=16
iter157 errorY= 0.5608, prior information ratio= 0, Bdiff= 4.97e-05, Bkappa=170.9;pos. col. U=15
iter158 errorY= 0.5608, prior information ratio= 0, Bdiff= 4.993e-05, Bkappa=171.4;pos. col. U=15
iter159 errorY= 0.5608, prior information ratio= 0, Bdiff= 5.015e-05, Bkappa=171.9;pos. col. U=15
Bdiff is not decreasing
Updating L3, current fraction= 0.5556, target=0.7
L3 is set to 0.000311 in 4 iterations
iter160 errorY= 0.5608, prior information ratio= 0, Bdiff= 5.036e-05, Bkappa=172.4;pos. col. U=18
Bdiff is not decreasing
iter161 errorY= 0.5608, prior information ratio= 0, Bdiff= 5.06e-05, Bkappa=172.9;pos. col. U=17
Bdiff is not decreasing
iter162 errorY= 0.5608, prior information ratio= 0, Bdiff= 5.085e-05, Bkappa=173.4;pos. col. U=17
Bdiff is not decreasing
iter163 errorY= 0.5608, prior information ratio= 0, Bdiff= 5.107e-05, Bkappa=173.9;pos. col. U=17
Bdiff is not decreasing
iter164 errorY= 0.5608, prior information ratio= 0, Bdiff= 5.131e-05, Bkappa=174.4;pos. col. U=17
Bdiff is not decreasing
converged at  iteration 164 Bdiff is not decreasing
There are 10  LVs with AUC>0.70



Removing 1 pathways with too few genesComputing SVD
Done
errorY (SVD based:best possible) = 0.3957
iter1 errorY= 0.5346, Bdiff= 0.3564, Bkappa=25.22
iter2 errorY= 0.4443, Bdiff= 0.07889, Bkappa=36.21
iter3 errorY= 0.4235, Bdiff= 0.02674, Bkappa=43.98
iter4 errorY= 0.4156, Bdiff= 0.0142, Bkappa=49.75
iter5 errorY= 0.4116, Bdiff= 0.009138, Bkappa=54.05
iter6 errorY= 0.409, Bdiff= 0.006569, Bkappa=57.77
iter7 errorY= 0.4073, Bdiff= 0.005149, Bkappa=61.24
iter8 errorY= 0.4061, Bdiff= 0.004307, Bkappa=64.21
iter9 errorY= 0.4052, Bdiff= 0.003747, Bkappa=67.74
iter10 errorY= 0.4045, Bdiff= 0.003244, Bkappa=71.41
iter11 errorY= 0.404, Bdiff= 0.002815, Bkappa=75.05
iter12 errorY= 0.4036, Bdiff= 0.002364, Bkappa=78.38
iter13 errorY= 0.4032, Bdiff= 0.001862, Bkappa=81.47
iter14 errorY= 0.4029, Bdiff= 0.001486, Bkappa=84.36
iter15 errorY= 0.4027, Bdiff= 0.001235, Bkappa=87.13
iter16 errorY= 0.4024, Bdiff= 0.001053, Bkappa=89.74
iter17 errorY= 0.4022, Bdiff= 0.0009096, Bkappa=92.19
iter18 errorY= 0.402, Bdiff= 0.0007927, Bkappa=94.5
iter19 errorY= 0.4018, Bdiff= 0.0006973, Bkappa=96.7
Updating L3, current fraction= 0, target=0.7
L3 is set to 0.000398 in 15 iterations
iter20 errorY= 0.4017, prior information ratio= 0, Bdiff= 0.0006184, Bkappa=98.84;pos. col. U=37
iter21 errorY= 0.4016, prior information ratio= 0, Bdiff= 0.0005542, Bkappa=100.8;pos. col. U=37
iter22 errorY= 0.4014, prior information ratio= 0, Bdiff= 5e-04, Bkappa=102.8;pos. col. U=37
iter23 errorY= 0.4013, prior information ratio= 0, Bdiff= 0.0004539, Bkappa=104.7;pos. col. U=37
iter24 errorY= 0.4012, prior information ratio= 0, Bdiff= 0.0004146, Bkappa=106.5;pos. col. U=36
iter25 errorY= 0.4011, prior information ratio= 0, Bdiff= 0.0003814, Bkappa=107.2;pos. col. U=36
iter26 errorY= 0.4011, prior information ratio= 0, Bdiff= 0.0003522, Bkappa=108.9;pos. col. U=35
iter27 errorY= 0.401, prior information ratio= 0, Bdiff= 0.0003272, Bkappa=110.6;pos. col. U=34
iter28 errorY= 0.4009, prior information ratio= 0, Bdiff= 0.0003057, Bkappa=112.2;pos. col. U=34
iter29 errorY= 0.4008, prior information ratio= 0, Bdiff= 0.0002869, Bkappa=113;pos. col. U=34
iter30 errorY= 0.4008, prior information ratio= 0, Bdiff= 0.0002703, Bkappa=114.5;pos. col. U=34
iter31 errorY= 0.4007, prior information ratio= 0, Bdiff= 0.0002556, Bkappa=115.8;pos. col. U=34
iter32 errorY= 0.4007, prior information ratio= 0, Bdiff= 0.0002424, Bkappa=117.3;pos. col. U=34
iter33 errorY= 0.4006, prior information ratio= 0, Bdiff= 0.0002306, Bkappa=118.9;pos. col. U=34
iter34 errorY= 0.4006, prior information ratio= 0, Bdiff= 0.00022, Bkappa=120.4;pos. col. U=32
iter35 errorY= 0.4005, prior information ratio= 0, Bdiff= 0.0002104, Bkappa=122;pos. col. U=32
iter36 errorY= 0.4005, prior information ratio= 0, Bdiff= 0.0002018, Bkappa=123.7;pos. col. U=32
iter37 errorY= 0.4004, prior information ratio= 0, Bdiff= 0.0001941, Bkappa=125.3;pos. col. U=33
iter38 errorY= 0.4004, prior information ratio= 0, Bdiff= 0.0001872, Bkappa=127;pos. col. U=33
iter39 errorY= 0.4004, prior information ratio= 0, Bdiff= 0.0001809, Bkappa=128.6;pos. col. U=33
Updating L3, current fraction= 0.6226, target=0.7
L3 is set to 0.000349 in 3 iterations
iter40 errorY= 0.4003, prior information ratio= 0, Bdiff= 0.0001752, Bkappa=130.2;pos. col. U=38
iter41 errorY= 0.4003, prior information ratio= 0, Bdiff= 0.0001699, Bkappa=133.1;pos. col. U=37
iter42 errorY= 0.4003, prior information ratio= 0, Bdiff= 0.000165, Bkappa=134.8;pos. col. U=35
iter43 errorY= 0.4002, prior information ratio= 0, Bdiff= 0.0001606, Bkappa=136.5;pos. col. U=35
iter44 errorY= 0.4002, prior information ratio= 0, Bdiff= 0.0001564, Bkappa=138.3;pos. col. U=35
iter45 errorY= 0.4002, prior information ratio= 0, Bdiff= 0.0001525, Bkappa=140.2;pos. col. U=35
iter46 errorY= 0.4001, prior information ratio= 0, Bdiff= 0.0001488, Bkappa=142;pos. col. U=35
iter47 errorY= 0.4001, prior information ratio= 0, Bdiff= 0.0001452, Bkappa=143.9;pos. col. U=35
iter48 errorY= 0.4001, prior information ratio= 0, Bdiff= 0.0001418, Bkappa=145.8;pos. col. U=35
iter49 errorY= 0.4001, prior information ratio= 0, Bdiff= 0.0001386, Bkappa=147.6;pos. col. U=35
iter50 errorY= 0.4, prior information ratio= 0, Bdiff= 0.0001355, Bkappa=149.5;pos. col. U=35
iter51 errorY= 0.4, prior information ratio= 0, Bdiff= 0.0001325, Bkappa=151.3;pos. col. U=35
iter52 errorY= 0.4, prior information ratio= 0, Bdiff= 0.0001295, Bkappa=153.1;pos. col. U=35
iter53 errorY= 0.4, prior information ratio= 0, Bdiff= 0.0001268, Bkappa=154.9;pos. col. U=36
iter54 errorY= 0.4, prior information ratio= 0, Bdiff= 0.0001241, Bkappa=156.7;pos. col. U=36
iter55 errorY= 0.3999, prior information ratio= 0, Bdiff= 0.0001216, Bkappa=158.4;pos. col. U=36
iter56 errorY= 0.3999, prior information ratio= 0, Bdiff= 0.0001191, Bkappa=160.2;pos. col. U=35
iter57 errorY= 0.3999, prior information ratio= 0, Bdiff= 0.0001168, Bkappa=162;pos. col. U=35
iter58 errorY= 0.3999, prior information ratio= 0, Bdiff= 0.0001147, Bkappa=163.7;pos. col. U=35
iter59 errorY= 0.3999, prior information ratio= 0, Bdiff= 0.0001127, Bkappa=165.5;pos. col. U=35
Updating L3, current fraction= 0.6604, target=0.7
L3 is set to 0.000305 in 3 iterations
iter60 errorY= 0.3999, prior information ratio= 0, Bdiff= 0.0001109, Bkappa=167.3;pos. col. U=38
iter61 errorY= 0.3998, prior information ratio= 0, Bdiff= 0.0001093, Bkappa=169.1;pos. col. U=38
iter62 errorY= 0.3998, prior information ratio= 0, Bdiff= 0.0001078, Bkappa=170.9;pos. col. U=38
iter63 errorY= 0.3998, prior information ratio= 0, Bdiff= 0.0001065, Bkappa=172.7;pos. col. U=38
iter64 errorY= 0.3998, prior information ratio= 0, Bdiff= 0.0001052, Bkappa=182.6;pos. col. U=38
iter65 errorY= 0.3998, prior information ratio= 0, Bdiff= 0.0001038, Bkappa=184.5;pos. col. U=38
iter66 errorY= 0.3998, prior information ratio= 0, Bdiff= 0.0001025, Bkappa=186.5;pos. col. U=38
iter67 errorY= 0.3998, prior information ratio= 0, Bdiff= 0.0001012, Bkappa=188.4;pos. col. U=38
iter68 errorY= 0.3997, prior information ratio= 0, Bdiff= 9.988e-05, Bkappa=190.3;pos. col. U=38
iter69 errorY= 0.3997, prior information ratio= 0, Bdiff= 9.855e-05, Bkappa=192.2;pos. col. U=38
iter70 errorY= 0.3997, prior information ratio= 0, Bdiff= 9.734e-05, Bkappa=194.1;pos. col. U=38
iter71 errorY= 0.3997, prior information ratio= 0, Bdiff= 9.621e-05, Bkappa=195.9;pos. col. U=38
iter72 errorY= 0.3997, prior information ratio= 0, Bdiff= 9.507e-05, Bkappa=197.8;pos. col. U=38
iter73 errorY= 0.3997, prior information ratio= 0, Bdiff= 9.389e-05, Bkappa=199.6;pos. col. U=38
iter74 errorY= 0.3997, prior information ratio= 0, Bdiff= 9.282e-05, Bkappa=201.4;pos. col. U=38
iter75 errorY= 0.3997, prior information ratio= 0, Bdiff= 9.188e-05, Bkappa=202.5;pos. col. U=38
iter76 errorY= 0.3997, prior information ratio= 0, Bdiff= 9.101e-05, Bkappa=204.2;pos. col. U=37
iter77 errorY= 0.3996, prior information ratio= 0, Bdiff= 9.023e-05, Bkappa=205.9;pos. col. U=37
iter78 errorY= 0.3996, prior information ratio= 0, Bdiff= 8.955e-05, Bkappa=161.9;pos. col. U=37
iter79 errorY= 0.3996, prior information ratio= 0, Bdiff= 8.894e-05, Bkappa=163.1;pos. col. U=37
Updating L3, current fraction= 0.6981, target=0.7
L3 not changed
iter80 errorY= 0.3996, prior information ratio= 0, Bdiff= 8.842e-05, Bkappa=164.3;pos. col. U=37
iter81 errorY= 0.3996, prior information ratio= 0, Bdiff= 8.799e-05, Bkappa=165.5;pos. col. U=37
iter82 errorY= 0.3996, prior information ratio= 0, Bdiff= 8.762e-05, Bkappa=166.8;pos. col. U=37
iter83 errorY= 0.3996, prior information ratio= 0, Bdiff= 8.731e-05, Bkappa=168;pos. col. U=37
iter84 errorY= 0.3996, prior information ratio= 0, Bdiff= 8.701e-05, Bkappa=169.3;pos. col. U=37
iter85 errorY= 0.3996, prior information ratio= 0, Bdiff= 8.675e-05, Bkappa=170.5;pos. col. U=37
iter86 errorY= 0.3996, prior information ratio= 0, Bdiff= 8.654e-05, Bkappa=171.7;pos. col. U=37
iter87 errorY= 0.3996, prior information ratio= 0, Bdiff= 8.637e-05, Bkappa=172.9;pos. col. U=37
iter88 errorY= 0.3995, prior information ratio= 0, Bdiff= 8.63e-05, Bkappa=174;pos. col. U=36
iter89 errorY= 0.3995, prior information ratio= 0, Bdiff= 8.627e-05, Bkappa=227.2;pos. col. U=36
iter90 errorY= 0.3995, prior information ratio= 0, Bdiff= 8.626e-05, Bkappa=228.9;pos. col. U=36
iter91 errorY= 0.3995, prior information ratio= 0, Bdiff= 8.631e-05, Bkappa=230.5;pos. col. U=36
iter92 errorY= 0.3995, prior information ratio= 0, Bdiff= 8.638e-05, Bkappa=232.1;pos. col. U=36
iter93 errorY= 0.3995, prior information ratio= 0, Bdiff= 8.65e-05, Bkappa=233.6;pos. col. U=35
iter94 errorY= 0.3995, prior information ratio= 0, Bdiff= 8.664e-05, Bkappa=212.4;pos. col. U=35
iter95 errorY= 0.3995, prior information ratio= 0, Bdiff= 8.685e-05, Bkappa=213.8;pos. col. U=35
iter96 errorY= 0.3995, prior information ratio= 0, Bdiff= 8.718e-05, Bkappa=215.1;pos. col. U=35
iter97 errorY= 0.3995, prior information ratio= 0, Bdiff= 8.751e-05, Bkappa=216.3;pos. col. U=35
iter98 errorY= 0.3995, prior information ratio= 0, Bdiff= 8.785e-05, Bkappa=226.5;pos. col. U=35
iter99 errorY= 0.3995, prior information ratio= 0, Bdiff= 8.818e-05, Bkappa=227.8;pos. col. U=35
Updating L3, current fraction= 0.6604, target=0.7
L3 is set to 0.000268 in 3 iterations
iter100 errorY= 0.3995, prior information ratio= 0, Bdiff= 8.858e-05, Bkappa=229;pos. col. U=38
iter101 errorY= 0.3995, prior information ratio= 0, Bdiff= 8.908e-05, Bkappa=230.2;pos. col. U=38
iter102 errorY= 0.3995, prior information ratio= 0, Bdiff= 8.963e-05, Bkappa=231.3;pos. col. U=38
iter103 errorY= 0.3995, prior information ratio= 0, Bdiff= 9.023e-05, Bkappa=232.5;pos. col. U=38
iter104 errorY= 0.3995, prior information ratio= 0, Bdiff= 9.1e-05, Bkappa=233.6;pos. col. U=38
iter105 errorY= 0.3995, prior information ratio= 0, Bdiff= 9.18e-05, Bkappa=234.7;pos. col. U=38
iter106 errorY= 0.3995, prior information ratio= 0, Bdiff= 9.263e-05, Bkappa=235.8;pos. col. U=38
iter107 errorY= 0.3995, prior information ratio= 0, Bdiff= 9.348e-05, Bkappa=236.8;pos. col. U=38
iter108 errorY= 0.3995, prior information ratio= 0, Bdiff= 9.444e-05, Bkappa=237.8;pos. col. U=38
iter109 errorY= 0.3995, prior information ratio= 0, Bdiff= 9.544e-05, Bkappa=238.8;pos. col. U=38
iter110 errorY= 0.3995, prior information ratio= 0, Bdiff= 9.66e-05, Bkappa=239.8;pos. col. U=38
iter111 errorY= 0.3995, prior information ratio= 0, Bdiff= 9.787e-05, Bkappa=242.6;pos. col. U=38
iter112 errorY= 0.3995, prior information ratio= 0, Bdiff= 9.922e-05, Bkappa=243.5;pos. col. U=38
iter113 errorY= 0.3995, prior information ratio= 0, Bdiff= 0.0001007, Bkappa=253.5;pos. col. U=38
iter114 errorY= 0.3995, prior information ratio= 0, Bdiff= 0.0001023, Bkappa=254.4;pos. col. U=38
iter115 errorY= 0.3995, prior information ratio= 0, Bdiff= 0.000104, Bkappa=255.3;pos. col. U=38
Bdiff is not decreasing
iter116 errorY= 0.3995, prior information ratio= 0, Bdiff= 0.0001052, Bkappa=256.1;pos. col. U=38
Bdiff is not decreasing
iter117 errorY= 0.3995, prior information ratio= 0, Bdiff= 0.0001065, Bkappa=256.9;pos. col. U=38
Bdiff is not decreasing
iter118 errorY= 0.3995, prior information ratio= 0, Bdiff= 0.0001073, Bkappa=257.7;pos. col. U=38
Bdiff is not decreasing
iter119 errorY= 0.3995, prior information ratio= 0, Bdiff= 0.000108, Bkappa=258.5;pos. col. U=38
Bdiff is not decreasing
Updating L3, current fraction= 0.717, target=0.7
L3 not changed
iter120 errorY= 0.3995, prior information ratio= 0, Bdiff= 0.0001089, Bkappa=259.2;pos. col. U=38
Bdiff is not decreasing
converged at  iteration 120 Bdiff is not decreasing
There are 19  LVs with AUC>0.70



Removing 1 pathways with too few genesComputing SVD
Done
errorY (SVD based:best possible) = 0.6015
iter1 errorY= 0.6609, Bdiff= 0.2018, Bkappa=7.217
iter2 errorY= 0.6295, Bdiff= 0.0416, Bkappa=9.899
iter3 errorY= 0.6211, Bdiff= 0.0188, Bkappa=12.97
iter4 errorY= 0.6173, Bdiff= 0.01074, Bkappa=15.45
iter5 errorY= 0.615, Bdiff= 0.006947, Bkappa=17.48
iter6 errorY= 0.6134, Bdiff= 0.004996, Bkappa=19.26
iter7 errorY= 0.6123, Bdiff= 0.003794, Bkappa=20.68
iter8 errorY= 0.6114, Bdiff= 0.002937, Bkappa=21.83
iter9 errorY= 0.6107, Bdiff= 0.00236, Bkappa=22.8
iter10 errorY= 0.6101, Bdiff= 0.001996, Bkappa=23.62
iter11 errorY= 0.6096, Bdiff= 0.001726, Bkappa=24.32
iter12 errorY= 0.6092, Bdiff= 0.001509, Bkappa=24.93
iter13 errorY= 0.6089, Bdiff= 0.001324, Bkappa=25.45
iter14 errorY= 0.6086, Bdiff= 0.001171, Bkappa=26.63
iter15 errorY= 0.6083, Bdiff= 0.001046, Bkappa=28.32
iter16 errorY= 0.6081, Bdiff= 0.0009445, Bkappa=30.04
iter17 errorY= 0.6079, Bdiff= 0.0008621, Bkappa=31.79
iter18 errorY= 0.6077, Bdiff= 0.000796, Bkappa=33.6
iter19 errorY= 0.6075, Bdiff= 0.0007405, Bkappa=35.57
Updating L3, current fraction= 0, target=0.7
L3 is set to 0.000398 in 15 iterations
iter20 errorY= 0.6074, prior information ratio= 0, Bdiff= 0.0006945, Bkappa=37.58;pos. col. U=16
iter21 errorY= 0.6072, prior information ratio= 0, Bdiff= 0.0006569, Bkappa=39.6;pos. col. U=16
iter22 errorY= 0.6071, prior information ratio= 0, Bdiff= 0.0006258, Bkappa=41.63;pos. col. U=16
iter23 errorY= 0.607, prior information ratio= 0, Bdiff= 0.000601, Bkappa=43.65;pos. col. U=15
iter24 errorY= 0.6069, prior information ratio= 0, Bdiff= 0.0005814, Bkappa=45.66;pos. col. U=14
iter25 errorY= 0.6068, prior information ratio= 0, Bdiff= 0.000565, Bkappa=47.62;pos. col. U=14
iter26 errorY= 0.6067, prior information ratio= 0, Bdiff= 0.0005473, Bkappa=49.51;pos. col. U=14
iter27 errorY= 0.6066, prior information ratio= 0, Bdiff= 0.0005259, Bkappa=51.32;pos. col. U=14
iter28 errorY= 0.6065, prior information ratio= 0, Bdiff= 0.0005046, Bkappa=53.02;pos. col. U=14
iter29 errorY= 0.6065, prior information ratio= 0, Bdiff= 0.0004835, Bkappa=54.59;pos. col. U=15
iter30 errorY= 0.6064, prior information ratio= 0, Bdiff= 0.0004601, Bkappa=56.01;pos. col. U=15
iter31 errorY= 0.6063, prior information ratio= 0, Bdiff= 0.0004272, Bkappa=57.3;pos. col. U=16
iter32 errorY= 0.6063, prior information ratio= 0, Bdiff= 0.0003682, Bkappa=58.51;pos. col. U=15
iter33 errorY= 0.6062, prior information ratio= 0, Bdiff= 0.0003233, Bkappa=59.66;pos. col. U=15
iter34 errorY= 0.6061, prior information ratio= 0, Bdiff= 0.0002888, Bkappa=60.75;pos. col. U=14
iter35 errorY= 0.606, prior information ratio= 0, Bdiff= 0.000263, Bkappa=61.81;pos. col. U=14
iter36 errorY= 0.606, prior information ratio= 0, Bdiff= 0.0002426, Bkappa=62.81;pos. col. U=14
iter37 errorY= 0.6059, prior information ratio= 0, Bdiff= 0.0002254, Bkappa=63.78;pos. col. U=14
iter38 errorY= 0.6058, prior information ratio= 0, Bdiff= 0.0002106, Bkappa=64.7;pos. col. U=14
iter39 errorY= 0.6058, prior information ratio= 0, Bdiff= 0.0001975, Bkappa=65.58;pos. col. U=14
Updating L3, current fraction= 0.6364, target=0.7
L3 is set to 0.000385 in 5 iterations
iter40 errorY= 0.6057, prior information ratio= 0, Bdiff= 0.0001859, Bkappa=66.43;pos. col. U=15
iter41 errorY= 0.6057, prior information ratio= 0, Bdiff= 0.0001757, Bkappa=61.57;pos. col. U=15
iter42 errorY= 0.6056, prior information ratio= 0, Bdiff= 0.0001664, Bkappa=62.27;pos. col. U=15
iter43 errorY= 0.6056, prior information ratio= 0, Bdiff= 0.0001581, Bkappa=62.95;pos. col. U=15
iter44 errorY= 0.6055, prior information ratio= 0, Bdiff= 0.0001506, Bkappa=63.6;pos. col. U=14
iter45 errorY= 0.6055, prior information ratio= 0, Bdiff= 0.0001435, Bkappa=64.22;pos. col. U=14
iter46 errorY= 0.6055, prior information ratio= 0, Bdiff= 0.0001367, Bkappa=64.81;pos. col. U=14
iter47 errorY= 0.6054, prior information ratio= 0, Bdiff= 0.0001301, Bkappa=65.37;pos. col. U=14
iter48 errorY= 0.6054, prior information ratio= 0, Bdiff= 0.0001238, Bkappa=68.5;pos. col. U=14
iter49 errorY= 0.6053, prior information ratio= 0, Bdiff= 0.0001177, Bkappa=69.05;pos. col. U=14
iter50 errorY= 0.6053, prior information ratio= 0, Bdiff= 0.000112, Bkappa=69.57;pos. col. U=14
iter51 errorY= 0.6053, prior information ratio= 0, Bdiff= 0.0001067, Bkappa=70.06;pos. col. U=15
iter52 errorY= 0.6052, prior information ratio= 0, Bdiff= 0.000102, Bkappa=70.52;pos. col. U=14
iter53 errorY= 0.6052, prior information ratio= 0, Bdiff= 9.769e-05, Bkappa=70.95;pos. col. U=14
iter54 errorY= 0.6052, prior information ratio= 0, Bdiff= 9.359e-05, Bkappa=71.36;pos. col. U=14
iter55 errorY= 0.6052, prior information ratio= 0, Bdiff= 8.974e-05, Bkappa=71.74;pos. col. U=14
iter56 errorY= 0.6051, prior information ratio= 0, Bdiff= 8.624e-05, Bkappa=72.11;pos. col. U=14
iter57 errorY= 0.6051, prior information ratio= 0, Bdiff= 8.3e-05, Bkappa=72.45;pos. col. U=14
iter58 errorY= 0.6051, prior information ratio= 0, Bdiff= 7.988e-05, Bkappa=72.77;pos. col. U=14
iter59 errorY= 0.6051, prior information ratio= 0, Bdiff= 7.691e-05, Bkappa=73.06;pos. col. U=14
Updating L3, current fraction= 0.6364, target=0.7
L3 is set to 0.000373 in 5 iterations
iter60 errorY= 0.605, prior information ratio= 0, Bdiff= 7.415e-05, Bkappa=73.35;pos. col. U=15
iter61 errorY= 0.605, prior information ratio= 0, Bdiff= 7.169e-05, Bkappa=70.44;pos. col. U=15
iter62 errorY= 0.605, prior information ratio= 0, Bdiff= 6.951e-05, Bkappa=70.67;pos. col. U=15
iter63 errorY= 0.605, prior information ratio= 0, Bdiff= 6.757e-05, Bkappa=70.89;pos. col. U=15
iter64 errorY= 0.605, prior information ratio= 0, Bdiff= 6.569e-05, Bkappa=71.11;pos. col. U=15
iter65 errorY= 0.6049, prior information ratio= 0, Bdiff= 6.389e-05, Bkappa=71.32;pos. col. U=15
iter66 errorY= 0.6049, prior information ratio= 0, Bdiff= 6.211e-05, Bkappa=71.53;pos. col. U=15
iter67 errorY= 0.6049, prior information ratio= 0, Bdiff= 6.039e-05, Bkappa=79.01;pos. col. U=15
iter68 errorY= 0.6049, prior information ratio= 0, Bdiff= 5.875e-05, Bkappa=79.26;pos. col. U=15
iter69 errorY= 0.6049, prior information ratio= 0, Bdiff= 5.718e-05, Bkappa=79.5;pos. col. U=15
iter70 errorY= 0.6048, prior information ratio= 0, Bdiff= 5.566e-05, Bkappa=79.74;pos. col. U=15
iter71 errorY= 0.6048, prior information ratio= 0, Bdiff= 5.419e-05, Bkappa=79.97;pos. col. U=15
iter72 errorY= 0.6048, prior information ratio= 0, Bdiff= 5.28e-05, Bkappa=80.2;pos. col. U=15
iter73 errorY= 0.6048, prior information ratio= 0, Bdiff= 5.15e-05, Bkappa=80.43;pos. col. U=15
iter74 errorY= 0.6048, prior information ratio= 0, Bdiff= 5.026e-05, Bkappa=80.65;pos. col. U=15
iter75 errorY= 0.6048, prior information ratio= 0, Bdiff= 4.907e-05, Bkappa=80.89;pos. col. U=15
iter76 errorY= 0.6048, prior information ratio= 0, Bdiff= 4.793e-05, Bkappa=81.16;pos. col. U=15
iter77 errorY= 0.6047, prior information ratio= 0, Bdiff= 4.683e-05, Bkappa=81.43;pos. col. U=15
iter78 errorY= 0.6047, prior information ratio= 0, Bdiff= 4.587e-05, Bkappa=81.69;pos. col. U=15
iter79 errorY= 0.6047, prior information ratio= 0, Bdiff= 4.494e-05, Bkappa=81.95;pos. col. U=15
Updating L3, current fraction= 0.6818, target=0.7
L3 not changed
iter80 errorY= 0.6047, prior information ratio= 0, Bdiff= 4.406e-05, Bkappa=82.21;pos. col. U=14
iter81 errorY= 0.6047, prior information ratio= 0, Bdiff= 4.324e-05, Bkappa=82.47;pos. col. U=14
iter82 errorY= 0.6047, prior information ratio= 0, Bdiff= 4.252e-05, Bkappa=82.72;pos. col. U=14
iter83 errorY= 0.6047, prior information ratio= 0, Bdiff= 4.182e-05, Bkappa=82.97;pos. col. U=14
iter84 errorY= 0.6047, prior information ratio= 0, Bdiff= 4.12e-05, Bkappa=83.23;pos. col. U=13
iter85 errorY= 0.6047, prior information ratio= 0, Bdiff= 4.06e-05, Bkappa=83.47;pos. col. U=13
iter86 errorY= 0.6047, prior information ratio= 0, Bdiff= 4.005e-05, Bkappa=83.72;pos. col. U=13
iter87 errorY= 0.6046, prior information ratio= 0, Bdiff= 3.955e-05, Bkappa=83.97;pos. col. U=13
iter88 errorY= 0.6046, prior information ratio= 0, Bdiff= 3.912e-05, Bkappa=84.21;pos. col. U=13
iter89 errorY= 0.6046, prior information ratio= 0, Bdiff= 3.869e-05, Bkappa=84.45;pos. col. U=13
iter90 errorY= 0.6046, prior information ratio= 0, Bdiff= 3.827e-05, Bkappa=84.68;pos. col. U=13
iter91 errorY= 0.6046, prior information ratio= 0, Bdiff= 3.787e-05, Bkappa=84.92;pos. col. U=13
iter92 errorY= 0.6046, prior information ratio= 0, Bdiff= 3.75e-05, Bkappa=85.14;pos. col. U=13
iter93 errorY= 0.6046, prior information ratio= 0, Bdiff= 3.714e-05, Bkappa=85.37;pos. col. U=13
iter94 errorY= 0.6046, prior information ratio= 0, Bdiff= 3.678e-05, Bkappa=85.58;pos. col. U=13
iter95 errorY= 0.6046, prior information ratio= 0, Bdiff= 3.64e-05, Bkappa=85.8;pos. col. U=13
iter96 errorY= 0.6046, prior information ratio= 0, Bdiff= 3.601e-05, Bkappa=86.01;pos. col. U=13
iter97 errorY= 0.6046, prior information ratio= 0, Bdiff= 3.563e-05, Bkappa=86.21;pos. col. U=13
iter98 errorY= 0.6046, prior information ratio= 0, Bdiff= 3.525e-05, Bkappa=86.42;pos. col. U=13
iter99 errorY= 0.6046, prior information ratio= 0, Bdiff= 3.489e-05, Bkappa=86.61;pos. col. U=13
Updating L3, current fraction= 0.5909, target=0.7
L3 is set to 0.00035 in 4 iterations
iter100 errorY= 0.6046, prior information ratio= 0, Bdiff= 3.456e-05, Bkappa=86.8;pos. col. U=16
iter101 errorY= 0.6045, prior information ratio= 0, Bdiff= 3.424e-05, Bkappa=86.99;pos. col. U=16
iter102 errorY= 0.6045, prior information ratio= 0, Bdiff= 3.393e-05, Bkappa=87.18;pos. col. U=16
iter103 errorY= 0.6045, prior information ratio= 0, Bdiff= 3.364e-05, Bkappa=87.37;pos. col. U=16
iter104 errorY= 0.6045, prior information ratio= 0, Bdiff= 3.337e-05, Bkappa=87.55;pos. col. U=16
iter105 errorY= 0.6045, prior information ratio= 0, Bdiff= 3.309e-05, Bkappa=87.74;pos. col. U=15
iter106 errorY= 0.6045, prior information ratio= 0, Bdiff= 3.282e-05, Bkappa=87.92;pos. col. U=14
iter107 errorY= 0.6045, prior information ratio= 0, Bdiff= 3.254e-05, Bkappa=88.1;pos. col. U=14
iter108 errorY= 0.6045, prior information ratio= 0, Bdiff= 3.227e-05, Bkappa=88.28;pos. col. U=14
iter109 errorY= 0.6045, prior information ratio= 0, Bdiff= 3.201e-05, Bkappa=88.45;pos. col. U=14
iter110 errorY= 0.6045, prior information ratio= 0, Bdiff= 3.177e-05, Bkappa=88.63;pos. col. U=14
iter111 errorY= 0.6045, prior information ratio= 0, Bdiff= 3.153e-05, Bkappa=88.8;pos. col. U=14
iter112 errorY= 0.6045, prior information ratio= 0, Bdiff= 3.131e-05, Bkappa=88.97;pos. col. U=14
iter113 errorY= 0.6045, prior information ratio= 0, Bdiff= 3.108e-05, Bkappa=89.15;pos. col. U=14
iter114 errorY= 0.6045, prior information ratio= 0, Bdiff= 3.085e-05, Bkappa=85.35;pos. col. U=14
iter115 errorY= 0.6045, prior information ratio= 0, Bdiff= 3.063e-05, Bkappa=85.51;pos. col. U=14
iter116 errorY= 0.6045, prior information ratio= 0, Bdiff= 3.041e-05, Bkappa=85.67;pos. col. U=14
iter117 errorY= 0.6045, prior information ratio= 0, Bdiff= 3.021e-05, Bkappa=85.83;pos. col. U=14
iter118 errorY= 0.6045, prior information ratio= 0, Bdiff= 3.002e-05, Bkappa=85.99;pos. col. U=14
iter119 errorY= 0.6045, prior information ratio= 0, Bdiff= 2.983e-05, Bkappa=86.16;pos. col. U=14
Updating L3, current fraction= 0.6364, target=0.7
L3 is set to 0.000329 in 4 iterations
iter120 errorY= 0.6045, prior information ratio= 0, Bdiff= 2.963e-05, Bkappa=86.32;pos. col. U=16
iter121 errorY= 0.6045, prior information ratio= 0, Bdiff= 2.945e-05, Bkappa=86.48;pos. col. U=16
iter122 errorY= 0.6045, prior information ratio= 0, Bdiff= 2.926e-05, Bkappa=86.64;pos. col. U=16
iter123 errorY= 0.6045, prior information ratio= 0, Bdiff= 2.906e-05, Bkappa=86.81;pos. col. U=16
iter124 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.887e-05, Bkappa=86.97;pos. col. U=16
iter125 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.869e-05, Bkappa=87.13;pos. col. U=16
iter126 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.849e-05, Bkappa=87.3;pos. col. U=16
iter127 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.83e-05, Bkappa=87.46;pos. col. U=16
iter128 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.811e-05, Bkappa=87.63;pos. col. U=16
iter129 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.792e-05, Bkappa=87.79;pos. col. U=16
iter130 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.773e-05, Bkappa=87.95;pos. col. U=16
iter131 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.752e-05, Bkappa=88.12;pos. col. U=16
iter132 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.732e-05, Bkappa=88.28;pos. col. U=15
iter133 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.713e-05, Bkappa=88.45;pos. col. U=15
iter134 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.694e-05, Bkappa=88.61;pos. col. U=15
iter135 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.675e-05, Bkappa=88.77;pos. col. U=15
iter136 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.656e-05, Bkappa=88.93;pos. col. U=15
iter137 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.638e-05, Bkappa=89.1;pos. col. U=15
iter138 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.622e-05, Bkappa=89.26;pos. col. U=15
iter139 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.606e-05, Bkappa=89.43;pos. col. U=15
Updating L3, current fraction= 0.6818, target=0.7
L3 not changed
iter140 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.59e-05, Bkappa=89.59;pos. col. U=15
iter141 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.575e-05, Bkappa=89.75;pos. col. U=15
iter142 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.56e-05, Bkappa=89.92;pos. col. U=15
iter143 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.546e-05, Bkappa=90.08;pos. col. U=15
iter144 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.531e-05, Bkappa=90.25;pos. col. U=14
iter145 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.517e-05, Bkappa=90.41;pos. col. U=14
iter146 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.503e-05, Bkappa=90.57;pos. col. U=14
iter147 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.489e-05, Bkappa=90.74;pos. col. U=14
iter148 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.474e-05, Bkappa=90.9;pos. col. U=14
iter149 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.459e-05, Bkappa=91.07;pos. col. U=14
iter150 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.444e-05, Bkappa=91.23;pos. col. U=14
iter151 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.429e-05, Bkappa=91.4;pos. col. U=14
iter152 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.414e-05, Bkappa=91.56;pos. col. U=14
iter153 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.4e-05, Bkappa=91.73;pos. col. U=14
iter154 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.385e-05, Bkappa=91.89;pos. col. U=14
iter155 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.37e-05, Bkappa=92.06;pos. col. U=14
iter156 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.356e-05, Bkappa=92.24;pos. col. U=14
iter157 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.343e-05, Bkappa=92.42;pos. col. U=14
iter158 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.331e-05, Bkappa=92.6;pos. col. U=13
iter159 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.32e-05, Bkappa=92.79;pos. col. U=13
Updating L3, current fraction= 0.5909, target=0.7
L3 is set to 0.000308 in 4 iterations
iter160 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.31e-05, Bkappa=92.97;pos. col. U=16
iter161 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.3e-05, Bkappa=93.15;pos. col. U=16
iter162 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.291e-05, Bkappa=93.34;pos. col. U=16
iter163 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.281e-05, Bkappa=93.52;pos. col. U=16
iter164 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.273e-05, Bkappa=93.7;pos. col. U=15
iter165 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.266e-05, Bkappa=93.89;pos. col. U=15
iter166 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.259e-05, Bkappa=94.07;pos. col. U=15
iter167 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.253e-05, Bkappa=94.26;pos. col. U=15
iter168 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.248e-05, Bkappa=94.44;pos. col. U=15
iter169 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.243e-05, Bkappa=94.63;pos. col. U=15
iter170 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.239e-05, Bkappa=94.81;pos. col. U=15
iter171 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.236e-05, Bkappa=101;pos. col. U=15
iter172 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.233e-05, Bkappa=101.2;pos. col. U=15
iter173 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.23e-05, Bkappa=101.4;pos. col. U=15
iter174 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.227e-05, Bkappa=101.6;pos. col. U=15
iter175 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.224e-05, Bkappa=101.9;pos. col. U=15
iter176 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.221e-05, Bkappa=102.1;pos. col. U=15
iter177 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.218e-05, Bkappa=102.3;pos. col. U=15
iter178 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.217e-05, Bkappa=102.5;pos. col. U=15
iter179 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.216e-05, Bkappa=102.8;pos. col. U=15
Updating L3, current fraction= 0.6818, target=0.7
L3 not changed
iter180 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.215e-05, Bkappa=103;pos. col. U=15
iter181 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.214e-05, Bkappa=103.2;pos. col. U=15
iter182 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.213e-05, Bkappa=103.4;pos. col. U=15
iter183 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.212e-05, Bkappa=103.7;pos. col. U=15
iter184 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.211e-05, Bkappa=103.9;pos. col. U=15
iter185 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.21e-05, Bkappa=104.1;pos. col. U=14
iter186 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.21e-05, Bkappa=104.3;pos. col. U=14
iter187 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.209e-05, Bkappa=104.6;pos. col. U=14
iter188 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.208e-05, Bkappa=104.8;pos. col. U=14
iter189 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.208e-05, Bkappa=105;pos. col. U=14
iter190 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.207e-05, Bkappa=105.3;pos. col. U=14
iter191 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.207e-05, Bkappa=105.5;pos. col. U=14
iter192 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.206e-05, Bkappa=105.7;pos. col. U=14
iter193 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.206e-05, Bkappa=105.9;pos. col. U=14
iter194 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.207e-05, Bkappa=106.2;pos. col. U=14
iter195 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.207e-05, Bkappa=106.4;pos. col. U=13
iter196 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.208e-05, Bkappa=106.6;pos. col. U=13
iter197 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.209e-05, Bkappa=106.9;pos. col. U=13
iter198 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.21e-05, Bkappa=107.1;pos. col. U=13
iter199 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.211e-05, Bkappa=107.3;pos. col. U=13
Updating L3, current fraction= 0.5909, target=0.7
L3 is set to 0.000289 in 4 iterations
iter200 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.214e-05, Bkappa=107.6;pos. col. U=15
iter201 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.216e-05, Bkappa=107.8;pos. col. U=15
iter202 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.219e-05, Bkappa=107.9;pos. col. U=15
iter203 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.224e-05, Bkappa=108.1;pos. col. U=15
iter204 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.229e-05, Bkappa=108.2;pos. col. U=15
iter205 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.233e-05, Bkappa=108.3;pos. col. U=15
iter206 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.238e-05, Bkappa=108.4;pos. col. U=15
iter207 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.243e-05, Bkappa=108.5;pos. col. U=15
iter208 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.248e-05, Bkappa=108.6;pos. col. U=15
iter209 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.253e-05, Bkappa=108.7;pos. col. U=15
iter210 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.26e-05, Bkappa=108.8;pos. col. U=15
iter211 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.266e-05, Bkappa=108.9;pos. col. U=15
iter212 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.272e-05, Bkappa=109;pos. col. U=15
iter213 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.279e-05, Bkappa=109.1;pos. col. U=15
iter214 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.285e-05, Bkappa=109.2;pos. col. U=15
Bdiff is not decreasing
iter215 errorY= 0.6044, prior information ratio= 0, Bdiff= 2.292e-05, Bkappa=109.3;pos. col. U=15
Bdiff is not decreasing
iter216 errorY= 0.6045, prior information ratio= 0, Bdiff= 2.299e-05, Bkappa=109.4;pos. col. U=15
Bdiff is not decreasing
iter217 errorY= 0.6045, prior information ratio= 0, Bdiff= 2.305e-05, Bkappa=109.5;pos. col. U=15
Bdiff is not decreasing
iter218 errorY= 0.6045, prior information ratio= 0, Bdiff= 2.312e-05, Bkappa=109.7;pos. col. U=15
Bdiff is not decreasing
iter219 errorY= 0.6045, prior information ratio= 0, Bdiff= 2.319e-05, Bkappa=109.8;pos. col. U=15
Bdiff is not decreasing
converged at  iteration 219 Bdiff is not decreasing
There are 8  LVs with AUC>0.70

saveRDS(penalty.zero.list, 
        file.path(results.dir, 
                  "subsampled_recount2_PLIER_model_L2_to_zero_500.RDS"))

Pathway coverage

pathway.coverage.list <- lapply(penalty.zero.list, GetPathwayCoverage)

coverage.df <- reshape2::melt(lapply(pathway.coverage.list, 
                                     function(x) x$pathway))
colnames(coverage.df) <- c("L2_zero_value", "seed")

Read in the results from the original subsampling experiment

coverage.file <- file.path("results", "30", "subsampled_pathway_coverage.tsv")
subsampling.coverage.df <- readr::read_tsv(coverage.file) %>%
  dplyr::filter(metric == "pathway coverage",
                sample_size == "500") %>%
  dplyr::select(value, seed)

Parsed with column specification:
cols(
  value = col_double(),
  metric = col_character(),
  seed = col_integer(),
  sample_size = col_integer()
)

colnames(subsampling.coverage.df)[1] <- "automatic_value"

Join and find the difference in pathway coverage between the “normal” model and the L2 = 0 model

coverage.df <- coverage.df %>%
  dplyr::mutate(seed = as.integer(seed)) %>%
  dplyr::inner_join(subsampling.coverage.df, by = "seed") %>%
  dplyr::select(seed, dplyr::everything()) %>%
  dplyr::mutate(difference = automatic_value - L2_zero_value)

coverage.df

readr::write_tsv(coverage.df, 
                 file.path(results.dir, "pathway_coverage_with_difference.tsv"))

LV-pathway association summaries

Let’s look at an example summary data.frame for L2 = 0

penalty.zero.list$`2876`$summary %>% 
  dplyr::filter(FDR < 0.05)

And another:

penalty.zero.list$`8828`$summary %>% 
  dplyr::filter(FDR < 0.05)

By going through the pages of these summaries, we can see that gene sets related to the spliceosome are woefully overrepresented.

Z matrix

One explanation for this is that the loadings, Z, are no longer capturing sparse combinations of pathways. We can check the number of positive entries for each latent variable (column).

example.z.matrix <- penalty.zero.list$`2876`$Z
positive.counts <- apply(example.z.matrix, 2, function(x) sum(x > 0))

Compare to the Z matrix for automatically selected L2 (same seed and therefore expression matrix)

auto.example.z.matrix <- models.list$`2876`$PLIER$Z
auto.positive.counts <- apply(auto.example.z.matrix, 2, function(x) sum(x > 0))

A data.frame for plotting

z.positive.df <- data.frame(
  positive_count = c(positive.counts, auto.positive.counts),
  model_type <- c(rep("L2 = 0", length(positive.counts)),
                  rep("L2 automatic", length(auto.positive.counts)))
)

Density plot of positive values

z.positive.df %>%
  ggplot2::ggplot(ggplot2::aes(x = positive_count, group = model_type,
                               fill = model_type)) +
  ggplot2::geom_density(alpha = 0.5) +
  ggplot2::theme_bw() +
  ggplot2::labs(x = "number of positive entries in Z",
                title = "Effect of L2 = 0 on Loadings") +
  ggplot2::theme(plot.title = ggplot2::element_text(hjust = 0.5),
                 text = ggplot2::element_text(size = 12)) +
  ggplot2::guides(fill = ggplot2::guide_legend(title = "parameter")) +
  ggplot2::scale_fill_manual(values = c("#FFFFFF", "#545454"))

ggplot2::ggsave(file.path(plot.dir, 
                          "L2_effect_on_Z_positive_entries_density.pdf"),
                plot = ggplot2::last_plot())

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