Mercurial > repos > fubar > digital_dge

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+<?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Galaxy rgDGE.py tool output - see http://g2.trac.bx.psu.edu/" />
+<title></title>
+<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
+</head>
+<body>
+<div class="document">
+
+<h2>Galaxy DGE outputs run at 09/09/2011 13:46:07<h2></br>Click on the images below to download high quality PDF versions</br>
+
+<table>
+
+<tr><td><a href="DGE.R">DGE.R</a></td></tr>
+<tr><td><a href="DGE_runner.log">DGE_runner.log</a></td></tr>
+<tr><td><a href="MDSplot.pdf"><img src="MDSplot.jpg" title="Click to download a print quality PDF of MDSplot.pdf" hspace="10" width="600"></a></td></tr>
+<tr><td><a href="Smearplot.pdf"><img src="Smearplot.jpg" title="Click to download a print quality PDF of Smearplot.pdf" hspace="10" width="600"></a></td></tr>
+</table>
+
+<h3>R log follows below</h3><hr><pre>
+
+## got TCols=2 5 8; CCols=1 4 7
+
+Loading required package: edgeR
+
+Loading required package: methods
+
+Calculating library sizes from column totals.
+
+Using grid search to estimate tagwise dispersion.
+
+Comparison of groups:  control - case
+
+Using grid search to estimate tagwise dispersion.
+
+Calculating library sizes from column totals.
+
+Calculating library sizes from column totals.
+
+Calculating library sizes from column totals.
+
+Calculating library sizes from column totals.
+
+Calculating library sizes from column totals.
+
+Calculating library sizes from column totals.
+
+Calculating library sizes from column totals.
+
+Calculating library sizes from column totals.
+
+Calculating library sizes from column totals.
+
+Calculating library sizes from column totals.
+
+Calculating library sizes from column totals.
+
+Calculating library sizes from column totals.
+
+Calculating library sizes from column totals.
+
+Calculating library sizes from column totals.
+
+Calculating library sizes from column totals.
+
+R version 2.13.0 (2011-04-13)
+
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+
+
+locale:
+
+ [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C
+
+ [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8
+
+ [5] LC_MONETARY=C              LC_MESSAGES=en_AU.UTF-8
+
+ [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C
+
+ [9] LC_ADDRESS=C               LC_TELEPHONE=C
+
+[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
+
+
+
+attached base packages:
+
+[1] methods   stats     graphics  grDevices utils     datasets  base
+
+
+
+other attached packages:
+
+[1] edgeR_2.2.5
+
+
+
+loaded via a namespace (and not attached):
+
+[1] limma_3.8.2
+
+GPL Ghostscript 8.70 (2009-07-31)
+
+Copyright (C) 2009 Artifex Software, Inc.  All rights reserved.
+
+This software comes with NO WARRANTY: see the file PUBLIC for details.
+
+Processing pages 1 through 1.
+
+Page 1
+
+Loading NimbusSanL-Regu font from /var/lib/defoma/gs.d/dirs/fonts/n019003l.pfb... 3949652 2206663 11805808 10453107 3 done.
+
+Loading NimbusSanL-Bold font from /var/lib/defoma/gs.d/dirs/fonts/n019004l.pfb... 3990644 2306771 11749008 10408350 3 done.
+
+GPL Ghostscript 8.70 (2009-07-31)
+
+Copyright (C) 2009 Artifex Software, Inc.  All rights reserved.
+
+This software comes with NO WARRANTY: see the file PUBLIC for details.
+
+Processing pages 1 through 1.
+
+Page 1
+
+Loading Dingbats font from /var/lib/defoma/gs.d/dirs/fonts/d050000l.pfb... 3906916 2148264 11805808 10452326 3 done.
+
+Loading NimbusSanL-Regu font from /var/lib/defoma/gs.d/dirs/fonts/n019003l.pfb... 3949652 2261866 11805808 10472695 3 done.
+
+Loading NimbusSanL-Bold font from /var/lib/defoma/gs.d/dirs/fonts/n019004l.pfb... 3990644 2361918 11749008 10427914 3 done.
+
+rgDGE.py CL = /opt/galaxy/tools/DGE/rgDGE.py --output_html /opt/galaxy/database/job_working_directory/2/dataset_3_files --input_matrix /tmp/tmpvhI4cN/database/files/000/dataset_1.dat --treatcols 3,6,9 --treatname case --ctrlcols 2,5,8 --ctrlname control --output_tab /tmp/tmpvhI4cN/database/files/000/dataset_2.dat --output_html /tmp/tmpvhI4cN/database/files/000/dataset_3.dat --output_dir /opt/galaxy/database/job_working_directory/2/dataset_3_files --method edgeR</br>
+
+DGE.R CL = Rscript /opt/galaxy/database/job_working_directory/2/dataset_3_files/DGE.R /opt/galaxy/database/job_working_directory/2/dataset_3_files /tmp/tmpvhI4cN/database/files/000/dataset_1.dat case 3,6,9 control 2,5,8 /tmp/tmpvhI4cN/database/files/000/dataset_2.dat</br>
+
+</pre>
+
+<b><a href="http://rgenetics.org">Galaxy Rgenetics</a> tool output rgDGE.py run at 09/09/2011 13:46:08</b><br/>
+</div></body></html>
+