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| author | joachim-jacob |
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| date | Wed, 17 Jul 2013 04:06:12 -0400 |
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<!DOCTYPE html> <!-- saved from url=(0014)about:internet --> <html> <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8"/> <title>VST transformation</title> <!-- Styles for R syntax highlighter --> <style type="text/css"> pre .operator, pre .paren { color: rgb(104, 118, 135) } pre .literal { color: rgb(88, 72, 246) } pre .number { color: rgb(0, 0, 205); } pre .comment { color: rgb(76, 136, 107); } pre .keyword { color: rgb(0, 0, 255); } pre .identifier { color: rgb(0, 0, 0); } pre .string { color: rgb(3, 106, 7); } </style> <!-- R syntax highlighter --> <script type="text/javascript"> var hljs=new function(){function m(p){return p.replace(/&/gm,"&").replace(/</gm,"<")}function f(r,q,p){return RegExp(q,"m"+(r.cI?"i":"")+(p?"g":""))}function b(r){for(var p=0;p<r.childNodes.length;p++){var q=r.childNodes[p];if(q.nodeName=="CODE"){return q}if(!(q.nodeType==3&&q.nodeValue.match(/\s+/))){break}}}function h(t,s){var p="";for(var 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hljs.initHighlightingOnLoad(); </script> <!-- MathJax scripts --> <script type="text/javascript" src="https://c328740.ssl.cf1.rackcdn.com/mathjax/2.0-latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> </script> <style type="text/css"> body, td { font-family: sans-serif; background-color: white; font-size: 12px; margin: 8px; } tt, code, pre { font-family: 'DejaVu Sans Mono', 'Droid Sans Mono', 'Lucida Console', Consolas, Monaco, monospace; } h1 { font-size:2.2em; } h2 { font-size:1.8em; } h3 { font-size:1.4em; } h4 { font-size:1.0em; } h5 { font-size:0.9em; } h6 { font-size:0.8em; } a:visited { color: rgb(50%, 0%, 50%); } pre { margin-top: 0; max-width: 95%; border: 1px solid #ccc; white-space: pre-wrap; } pre code { display: block; padding: 0.5em; } code.r, code.cpp { background-color: #F8F8F8; } table, td, th { border: none; } blockquote { color:#666666; margin:0; padding-left: 1em; border-left: 0.5em #EEE solid; } hr { height: 0px; border-bottom: none; border-top-width: thin; border-top-style: dotted; border-top-color: #999999; } @media print { * { background: transparent !important; color: black !important; filter:none !important; -ms-filter: none !important; } body { font-size:12pt; max-width:100%; } a, a:visited { text-decoration: underline; } hr { visibility: hidden; page-break-before: always; } pre, blockquote { padding-right: 1em; page-break-inside: avoid; } tr, img { page-break-inside: avoid; } img { max-width: 100% !important; } @page :left { margin: 15mm 20mm 15mm 10mm; } @page :right { margin: 15mm 10mm 15mm 20mm; } p, h2, h3 { orphans: 3; widows: 3; } h2, h3 { page-break-after: avoid; } } </style> </head> <body> <h1>VST transformation</h1> <hr/> <p>Loading the R environment</p> <pre><code class="r">library("DESeq") library(reshape) library(ggplot2) </code></pre> <p>Reading input</p> <pre><code class="r">filename = "counttable1.tsv" raw_counts = read.csv(filename, sep = "\t", header = T, row.names = 1, stringsAsFactors = F) raw_counts_deseqct = newCountDataSet(raw_counts[, c(1, 2)], factor(c("can", "can"))) </code></pre> <hr/> <p>Performing VST transformation</p> <pre><code class="r">raw_counts_deseqct = newCountDataSet(raw_counts[, c(1, 2)], factor(c("can", "can"))) raw_counts_deseqct = estimateSizeFactors(raw_counts_deseqct) raw_counts_deseqctBlind = estimateDispersions(raw_counts_deseqct, method = "blind") vsd = varianceStabilizingTransformation(raw_counts_deseqctBlind) vst_raw_counts = exprs(vsd) </code></pre> <hr/> <pre><code class="r">write.table(vst_raw_counts, file = "vst_transf_tabout.txt", sep = "\t", quote = F, col.names = NA, row.names = TRUE) head(vst_raw_counts) </code></pre> <pre><code>## can_1 can_2 ## FBgn0000003 10.095 10.155 ## FBgn0000008 11.078 11.130 ## FBgn0000014 9.834 9.921 ## FBgn0000015 9.834 9.834 ## FBgn0000017 12.450 12.406 ## FBgn0000018 10.414 10.429 </code></pre> <pre><code class="r">vst_raw_counts_melted = melt(vst_raw_counts) ggplot(data = vst_raw_counts_melted, aes(value, colour = X2)) </code></pre> <pre><code>## Error: No layers in plot </code></pre> <pre><code class="r">+geom_density(alpha = 0.2) </code></pre> <pre><code>## Error: invalid argument to unary operator </code></pre> <pre><code class="r">+labs(x = "VST of counts") </code></pre> <pre><code>## Error: invalid argument to unary operator </code></pre> <pre><code class="r"> for (sample in colnames(vst_raw_counts)) { hist(vst_raw_counts[, colnames(vst_raw_counts) == sample], main = paste("Sample", sample), breaks = 80, xlab = "VST counts") } </code></pre> <p><img 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alt="plot of chunk plotting and writing"/> <img 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alt="plot of chunk plotting and writing"/> </p> <hr/> <hr/> <p>Logging R environment</p> <pre><code class="r">sessionInfo() </code></pre> <pre><code>## R version 3.0.1 (2013-05-16) ## Platform: x86_64-pc-linux-gnu (64-bit) ## ## locale: ## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C ## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 ## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 ## [7] LC_PAPER=C LC_NAME=C ## [9] LC_ADDRESS=C LC_TELEPHONE=C ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C ## ## attached base packages: ## [1] parallel stats graphics grDevices utils datasets methods ## [8] base ## ## other attached packages: ## [1] ggplot2_0.9.3.1 reshape_0.8.4 plyr_1.8 ## [4] DESeq_1.12.0 lattice_0.20-15 locfit_1.5-9.1 ## [7] Biobase_2.20.1 BiocGenerics_0.6.0 markdown_0.6.1 ## [10] knitr_1.2 ## ## loaded via a namespace (and not attached): ## [1] annotate_1.38.0 AnnotationDbi_1.22.6 colorspace_1.2-2 ## [4] DBI_0.2-7 dichromat_2.0-0 digest_0.6.3 ## [7] evaluate_0.4.4 formatR_0.8 genefilter_1.42.0 ## [10] geneplotter_1.38.0 grid_3.0.1 gtable_0.1.2 ## [13] IRanges_1.18.2 labeling_0.2 MASS_7.3-27 ## [16] munsell_0.4.2 proto_0.3-10 RColorBrewer_1.0-5 ## [19] reshape2_1.2.2 RSQLite_0.11.4 scales_0.2.3 ## [22] splines_3.0.1 stats4_3.0.1 stringr_0.6.2 ## [25] survival_2.37-4 tools_3.0.1 XML_3.98-1.1 ## [28] xtable_1.7-1 </code></pre> <hr/> </body> </html>