Galaxy DGE outputs run at 09/09/2011 13:46:07Click on the images below to download high quality PDF versions
+
+
| DGE.R |
| DGE_runner.log |
 |
 |
R log follows below
+ +## 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 + +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 + ++ +Galaxy Rgenetics tool output rgDGE.py run at 09/09/2011 13:46:08
+