Mercurial > repos > fubar > digital_dge
view DGEtest1out.html @ 3:dd69d0a22d92 default tip
Initial checkin of test data for DGE - move to your test-data directory for tests to work
| author | fubar |
|---|---|
| date | Fri, 09 Sep 2011 01:11:38 -0400 |
| parents | e019d4e43537 |
| children |
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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>