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annotate DGEtest1out.html @ 2:e019d4e43537

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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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1 <?xml version="1.0" encoding="utf-8" ?>
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2 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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3 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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4 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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5 <meta name="generator" content="Galaxy rgDGE.py tool output - see http://g2.trac.bx.psu.edu/" />
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6 <title></title>
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7 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
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8 </head>
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9 <body>
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10 <div class="document">
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11
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12 <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>
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14 <table>
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15
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16 <tr><td><a href="DGE.R">DGE.R</a></td></tr>
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17 <tr><td><a href="DGE_runner.log">DGE_runner.log</a></td></tr>
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18 <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>
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19 <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>
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20 </table>
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21
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22 <h3>R log follows below</h3><hr><pre>
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24 ## got TCols=2 5 8; CCols=1 4 7
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26 Loading required package: edgeR
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28 Loading required package: methods
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29
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30 Calculating library sizes from column totals.
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31
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32 Using grid search to estimate tagwise dispersion.
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34 Comparison of groups: control - case
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36 Using grid search to estimate tagwise dispersion.
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37
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38 Calculating library sizes from column totals.
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40 Calculating library sizes from column totals.
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42 Calculating library sizes from column totals.
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44 Calculating library sizes from column totals.
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46 Calculating library sizes from column totals.
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48 Calculating library sizes from column totals.
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50 Calculating library sizes from column totals.
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52 Calculating library sizes from column totals.
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54 Calculating library sizes from column totals.
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56 Calculating library sizes from column totals.
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58 Calculating library sizes from column totals.
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60 Calculating library sizes from column totals.
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62 Calculating library sizes from column totals.
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64 Calculating library sizes from column totals.
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66 Calculating library sizes from column totals.
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68 R version 2.13.0 (2011-04-13)
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69
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70 Platform: x86_64-unknown-linux-gnu (64-bit)
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76 [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
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78 [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
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80 [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8
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82 [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
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84 [9] LC_ADDRESS=C LC_TELEPHONE=C
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86 [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
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90 attached base packages:
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91
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92 [1] methods stats graphics grDevices utils datasets base
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96 other attached packages:
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98 [1] edgeR_2.2.5
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102 loaded via a namespace (and not attached):
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103
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104 [1] limma_3.8.2
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106 GPL Ghostscript 8.70 (2009-07-31)
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107
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108 Copyright (C) 2009 Artifex Software, Inc. All rights reserved.
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109
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110 This software comes with NO WARRANTY: see the file PUBLIC for details.
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111
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112 Processing pages 1 through 1.
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114 Page 1
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116 Loading NimbusSanL-Regu font from /var/lib/defoma/gs.d/dirs/fonts/n019003l.pfb... 3949652 2206663 11805808 10453107 3 done.
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118 Loading NimbusSanL-Bold font from /var/lib/defoma/gs.d/dirs/fonts/n019004l.pfb... 3990644 2306771 11749008 10408350 3 done.
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120 GPL Ghostscript 8.70 (2009-07-31)
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122 Copyright (C) 2009 Artifex Software, Inc. All rights reserved.
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124 This software comes with NO WARRANTY: see the file PUBLIC for details.
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125
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126 Processing pages 1 through 1.
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128 Page 1
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130 Loading Dingbats font from /var/lib/defoma/gs.d/dirs/fonts/d050000l.pfb... 3906916 2148264 11805808 10452326 3 done.
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132 Loading NimbusSanL-Regu font from /var/lib/defoma/gs.d/dirs/fonts/n019003l.pfb... 3949652 2261866 11805808 10472695 3 done.
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134 Loading NimbusSanL-Bold font from /var/lib/defoma/gs.d/dirs/fonts/n019004l.pfb... 3990644 2361918 11749008 10427914 3 done.
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135
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136 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>
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137
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138 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>
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139
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140 </pre>
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141
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142 <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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143 </div></body></html>
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