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Initial checkin of test files - move to test-data when installed.
author fubar
date Fri, 09 Sep 2011 01:10:19 -0400
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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.

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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.

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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/>
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