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<h1 class="title toc-ignore">Brain Tumor-Flash</h1>
<h4 class="author"><em>Yuxin Zou</em></h4>
<h4 class="date"><em>2018-2-20</em></h4>
</div>
<!-- Update knitr chunk options -->
<!-- Insert the date the file was last updated -->
<p><strong>Last updated:</strong> 2018-03-06</p>
<!-- Insert the code version (Git commit SHA1) if Git repository exists and R
package git2r is installed -->
<p><strong>Code version:</strong> e16e34a</p>
<pre><code>R.matlab v3.6.1 (2016-10-19) successfully loaded. See ?R.matlab for help.</code></pre>
<pre><code>
Attaching package: 'R.matlab'</code></pre>
<pre><code>The following objects are masked from 'package:base':
getOption, isOpen</code></pre>
<p>Brain Tumor data:</p>
<p>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.</p>
<pre class="r"><code>data = readMat('../data/BrainTumor.mat')
data = data$Y</code></pre>
<p>Flash:</p>
<pre class="r"><code>flash.data = flash_set_data(data)
f = flash(flash.data, greedy = TRUE, backfit = TRUE)
saveRDS(f, '../output/BrainTumorVarCol.rds')</code></pre>
<pre class="r"><code>Factors = flash_get_ldf(fmodel)$f
pve.order = order(flash_get_pve(fmodel), decreasing = TRUE)</code></pre>
<pre class="r"><code>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="")
}</code></pre>
<p><img src="figure/Flash_Brain.Rmd/unnamed-chunk-7-1.png" width="672" style="display: block; margin: auto;" /><img src="figure/Flash_Brain.Rmd/unnamed-chunk-7-2.png" width="672" style="display: block; margin: auto;" /></p>
<p>Flash again on the loading matrix</p>
<pre class="r"><code>flash.loading = flash_set_data(fmodel$EL[,1:9])
flmodel = flash(flash.loading, greedy = TRUE, backfit = TRUE)</code></pre>
<pre><code>fitting factor/loading 1</code></pre>
<p>The flash prefers the rank 0 model. There is no hidden structure in the loading matrix.</p>
<div id="session-information" class="section level1">
<h1>Session information</h1>
<!-- Insert the session information into the document -->
<pre class="r"><code>sessionInfo()</code></pre>
<pre><code>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 </code></pre>
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