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comparison 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:ba8c9980350b 2:e019d4e43537
1 <?xml version="1.0" encoding="utf-8" ?>
2 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
3 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
4 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
5 <meta name="generator" content="Galaxy rgDGE.py tool output - see http://g2.trac.bx.psu.edu/" />
6 <title></title>
7 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
8 </head>
9 <body>
10 <div class="document">
11
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>
13
14 <table>
15
16 <tr><td><a href="DGE.R">DGE.R</a></td></tr>
17 <tr><td><a href="DGE_runner.log">DGE_runner.log</a></td></tr>
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>
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>
20 </table>
21
22 <h3>R log follows below</h3><hr><pre>
23
24 ## got TCols=2 5 8; CCols=1 4 7
25
26 Loading required package: edgeR
27
28 Loading required package: methods
29
30 Calculating library sizes from column totals.
31
32 Using grid search to estimate tagwise dispersion.
33
34 Comparison of groups: control - case
35
36 Using grid search to estimate tagwise dispersion.
37
38 Calculating library sizes from column totals.
39
40 Calculating library sizes from column totals.
41
42 Calculating library sizes from column totals.
43
44 Calculating library sizes from column totals.
45
46 Calculating library sizes from column totals.
47
48 Calculating library sizes from column totals.
49
50 Calculating library sizes from column totals.
51
52 Calculating library sizes from column totals.
53
54 Calculating library sizes from column totals.
55
56 Calculating library sizes from column totals.
57
58 Calculating library sizes from column totals.
59
60 Calculating library sizes from column totals.
61
62 Calculating library sizes from column totals.
63
64 Calculating library sizes from column totals.
65
66 Calculating library sizes from column totals.
67
68 R version 2.13.0 (2011-04-13)
69
70 Platform: x86_64-unknown-linux-gnu (64-bit)
71
72
73
74 locale:
75
76 [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
77
78 [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
79
80 [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8
81
82 [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
83
84 [9] LC_ADDRESS=C LC_TELEPHONE=C
85
86 [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
87
88
89
90 attached base packages:
91
92 [1] methods stats graphics grDevices utils datasets base
93
94
95
96 other attached packages:
97
98 [1] edgeR_2.2.5
99
100
101
102 loaded via a namespace (and not attached):
103
104 [1] limma_3.8.2
105
106 GPL Ghostscript 8.70 (2009-07-31)
107
108 Copyright (C) 2009 Artifex Software, Inc. All rights reserved.
109
110 This software comes with NO WARRANTY: see the file PUBLIC for details.
111
112 Processing pages 1 through 1.
113
114 Page 1
115
116 Loading NimbusSanL-Regu font from /var/lib/defoma/gs.d/dirs/fonts/n019003l.pfb... 3949652 2206663 11805808 10453107 3 done.
117
118 Loading NimbusSanL-Bold font from /var/lib/defoma/gs.d/dirs/fonts/n019004l.pfb... 3990644 2306771 11749008 10408350 3 done.
119
120 GPL Ghostscript 8.70 (2009-07-31)
121
122 Copyright (C) 2009 Artifex Software, Inc. All rights reserved.
123
124 This software comes with NO WARRANTY: see the file PUBLIC for details.
125
126 Processing pages 1 through 1.
127
128 Page 1
129
130 Loading Dingbats font from /var/lib/defoma/gs.d/dirs/fonts/d050000l.pfb... 3906916 2148264 11805808 10452326 3 done.
131
132 Loading NimbusSanL-Regu font from /var/lib/defoma/gs.d/dirs/fonts/n019003l.pfb... 3949652 2261866 11805808 10472695 3 done.
133
134 Loading NimbusSanL-Bold font from /var/lib/defoma/gs.d/dirs/fonts/n019004l.pfb... 3990644 2361918 11749008 10427914 3 done.
135
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>
137
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>
139
140 </pre>
141
142 <b><a href="http://rgenetics.org">Galaxy Rgenetics</a> tool output rgDGE.py run at 09/09/2011 13:46:08</b><br/>
143 </div></body></html>
144