| GDAC_mirnaTopgenesforCluster1 expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PANCAN12-TP/3025376/2.GDAC_MergeDataFiles.Finished/PANCAN12-TP.mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.txt |
| GDAC_mirnaTopgenesforCluster1 selectedgenes | 150 |
| GDAC_ConsensusClustering2 clustering algorithm | HIERARCHICAL |
| GDAC_ConsensusClustering2 cluster by | |
| GDAC_ConsensusClustering2 distance measure | PEARSON |
| GDAC_ConsensusClustering2 normalize type | |
| GDAC_selectBestcluster3 measure | Pearson |
| GDAC_selectBestcluster3 output | PANCAN12-TP |
| GDAC_selectBestcluster3 inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PANCAN12-TP/3025376/2.GDAC_MergeDataFiles.Finished/PANCAN12-TP.mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.txt |
| Execution Times: | |
| Submitted: | 14:29:09 02-05-13 |
| Completed: | |
| Elapsed: | 02 hrs 30 mins 15 secs |
step 1. GDAC_mirnaTopgenesforCluster [id: 395968] This module can be used to selecte top genes with most variation, convert file to gct format, as well as imput missing value
urn:lsid:broadinstitute.org:cancer.genome.analysis:00284:3
| expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PANCAN12-TP/3025376/2.GDAC_MergeDataFiles.Finished/PANCAN12-TP.mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.txt |
| selectedgenes | 150 |
| outputprefix | outputprefix |
| Output Files: | |
| outputprefix.expclu.gct | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 14:29:09 02-05-13 |
| Completed: | 16:43:34 02-05-13 |
| Elapsed: | 02 hrs 14 mins 24 secs |
step 2. GDAC_ConsensusClustering [id: 395969] Resampling-based clustering method
urn:lsid:broadinstitute.org:cancer.genome.analysis:00158:6
| input filename | outputprefix.expclu.gct |
| kmax | 8 |
| resampling iterations | 20 |
| seed value | 12345 |
| clustering algorithm | HIERARCHICAL |
| cluster by | |
| distance measure | PEARSON |
| resample | subsample |
| merge type | average |
| descent iterations | 2000 |
| output stub | <input.filename_basename> |
| normalize type | |
| normalization iterations | 0 |
| create heat map | -p |
| heat map size | 2 |
| Execution Times: | |
| Submitted: | 14:29:09 02-05-13 |
| Completed: | 16:56:42 02-05-13 |
| Elapsed: | 02 hrs 27 mins 32 secs |
step 3. GDAC_selectBestcluster [id: 395970]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00207:32
| measure | Pearson |
| inputexp | outputprefix.expclu.gct |
| output | PANCAN12-TP |
| file clu 2 | outputprefix.expclu.sub454.2.clu |
| file clu 3 | outputprefix.expclu.sub454.3.clu |
| file clu 4 | outputprefix.expclu.sub454.4.clu |
| file clu 5 | outputprefix.expclu.sub454.5.clu |
| file clu 6 | outputprefix.expclu.sub454.6.clu |
| file clu 7 | outputprefix.expclu.sub454.7.clu |
| file clu 8 | outputprefix.expclu.sub454.8.clu |
| inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PANCAN12-TP/3025376/2.GDAC_MergeDataFiles.Finished/PANCAN12-TP.mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.txt |
| Execution Times: | |
| Submitted: | 14:29:09 02-05-13 |
| Completed: | 16:58:42 02-05-13 |
| Elapsed: | 02 hrs 29 mins 32 secs |
step 4. GDAC_mirnaConsensusReport [id: 395971]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00278:13
| kclus | PANCAN12-TP.silfig.png |
| markers | PANCAN12-TP.subclassmarkers.txt |
| bestclu | PANCAN12-TP.bestclus.txt |
| allcluster | PANCAN12-TP.allclusters.txt |
| cormatrix | PANCAN12-TP.cormatrix.png |
| file gif 2 | outputprefix.expclu.sub454.srt.2.gif |
| file gif 3 | outputprefix.expclu.sub454.srt.3.gif |
| file gif 4 | outputprefix.expclu.sub454.srt.4.gif |
| file gif 5 | outputprefix.expclu.sub454.srt.5.gif |
| file gif 6 | outputprefix.expclu.sub454.srt.6.gif |
| file gif 7 | outputprefix.expclu.sub454.srt.7.gif |
| file gif 8 | outputprefix.expclu.sub454.srt.8.gif |
| expdata | outputprefix.expclu.gct |
| markersP | PANCAN12-TP.seclectedSubclassmarkers.txt |
| heatmap | PANCAN12-TP.geneheatmap.png |
| heatmapall | PANCAN12-TP.geneheatmaptopgenes.png |
| Output Files: | |
| nozzle.html | |
| .lsf.out | |
| nozzle.RData | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 14:29:09 02-05-13 |
| Completed: | 16:59:22 02-05-13 |
| Elapsed: | 02 hrs 30 mins 12 secs |
