Last updated: 2018-03-06

Code version: e16e34a

R.matlab v3.6.1 (2016-10-19) successfully loaded. See ?R.matlab for help.

Attaching package: 'R.matlab'
The following objects are masked from 'package:base':

    getOption, isOpen

Brain Tumor data:

The data consist of micro array gene expression measurements on 43 brain tumors of four types, together with 356 additional variables related to the expression data. We pre-processed the data by centering the data by column.

data = readMat('../data/BrainTumor.mat')
data = data$Y

Flash:

flash.data = flash_set_data(data)
f = flash(flash.data, greedy = TRUE, backfit = TRUE)

saveRDS(f, '../output/BrainTumorVarCol.rds')
Factors = flash_get_ldf(fmodel)$f
pve.order = order(flash_get_pve(fmodel), decreasing = TRUE)
par(mar=c(1,1,1,1))
par(mfrow=c(3,2))

for(i in pve.order){
  barplot(Factors[,i], main=paste0('Factor ',i, ' pve= ', round(flash_get_pve(fmodel)[i],3)), las=2, cex.names = 0.4, names="")
}

Flash again on the loading matrix

flash.loading = flash_set_data(fmodel$EL[,1:9])
flmodel = flash(flash.loading, greedy = TRUE, backfit = TRUE)
fitting factor/loading 1

The flash prefers the rank 0 model. There is no hidden structure in the loading matrix.

Session information

sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.3

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] R.matlab_3.6.1 flashr_0.5-6  

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.15      compiler_3.4.3    git2r_0.20.0     
 [4] plyr_1.8.4        R.utils_2.6.0     R.methodsS3_1.7.1
 [7] iterators_1.0.9   tools_3.4.3       digest_0.6.13    
[10] evaluate_0.10.1   tibble_1.3.4      gtable_0.2.0     
[13] lattice_0.20-35   rlang_0.1.6       Matrix_1.2-12    
[16] foreach_1.4.4     yaml_2.1.17       parallel_3.4.3   
[19] ebnm_0.1-10       stringr_1.3.0     knitr_1.20       
[22] rprojroot_1.2     grid_3.4.3        rmarkdown_1.8    
[25] ggplot2_2.2.1     ashr_2.2-7        magrittr_1.5     
[28] backports_1.1.2   scales_0.5.0      codetools_0.2-15 
[31] htmltools_0.3.6   MASS_7.3-47       assertthat_0.2.0 
[34] softImpute_1.4    colorspace_1.3-2  stringi_1.1.6    
[37] lazyeval_0.2.1    pscl_1.5.2        doParallel_1.0.11
[40] munsell_0.4.3     truncnorm_1.0-8   SQUAREM_2017.10-1
[43] R.oo_1.21.0

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