| GDAC_mirnaTopgenesforCluster1 expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PANCANCER/1669567/2.GDAC_MergeDataFiles.Finished/PANCANCER.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 | PANCANCER |
| GDAC_selectBestcluster3 inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PANCANCER/1669567/2.GDAC_MergeDataFiles.Finished/PANCANCER.mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.txt |
| Execution Times: | |
| Submitted: | 12:34:57 28-08-12 |
| Completed: | |
| Elapsed: | 00 hrs 13 mins 55 secs |
step 1. GDAC_mirnaTopgenesforCluster [id: 158500] 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/PANCANCER/1669567/2.GDAC_MergeDataFiles.Finished/PANCANCER.mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.txt |
| selectedgenes | 150 |
| outputprefix | outputprefix |
| Output Files: | |
| outputprefix.expclu.gct | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 12:34:58 28-08-12 |
| Completed: | 12:35:30 28-08-12 |
| Elapsed: | 00 hrs 00 mins 32 secs |
step 2. GDAC_ConsensusClustering [id: 158501] 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: | 12:34:58 28-08-12 |
| Completed: | 12:48:00 28-08-12 |
| Elapsed: | 00 hrs 13 mins 02 secs |
step 3. GDAC_selectBestcluster [id: 158502]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00207:32
| measure | Pearson |
| inputexp | outputprefix.expclu.gct |
| output | PANCANCER |
| file clu 2 | outputprefix.expclu.sub456.2.clu |
| file clu 3 | outputprefix.expclu.sub456.3.clu |
| file clu 4 | outputprefix.expclu.sub456.4.clu |
| file clu 5 | outputprefix.expclu.sub456.5.clu |
| file clu 6 | outputprefix.expclu.sub456.6.clu |
| file clu 7 | outputprefix.expclu.sub456.7.clu |
| file clu 8 | outputprefix.expclu.sub456.8.clu |
| inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PANCANCER/1669567/2.GDAC_MergeDataFiles.Finished/PANCANCER.mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.txt |
| Execution Times: | |
| Submitted: | 12:34:58 28-08-12 |
| Completed: | 12:48:34 28-08-12 |
| Elapsed: | 00 hrs 13 mins 36 secs |
step 4. GDAC_mirnaConsensusReport [id: 158503]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00278:13
| kclus | PANCANCER.silfig.png |
| markers | PANCANCER.subclassmarkers.txt |
| bestclu | PANCANCER.bestclus.txt |
| allcluster | PANCANCER.allclusters.txt |
| cormatrix | PANCANCER.cormatrix.png |
| file gif 2 | outputprefix.expclu.sub456.srt.2.gif |
| file gif 3 | outputprefix.expclu.sub456.srt.3.gif |
| file gif 4 | outputprefix.expclu.sub456.srt.4.gif |
| file gif 5 | outputprefix.expclu.sub456.srt.5.gif |
| file gif 6 | outputprefix.expclu.sub456.srt.6.gif |
| file gif 7 | outputprefix.expclu.sub456.srt.7.gif |
| file gif 8 | outputprefix.expclu.sub456.srt.8.gif |
| expdata | outputprefix.expclu.gct |
| markersP | PANCANCER.seclectedSubclassmarkers.txt |
| heatmap | PANCANCER.geneheatmap.png |
| heatmapall | PANCANCER.geneheatmaptopgenes.png |
| Output Files: | |
| nozzle.html | |
| .lsf.out | |
| nozzle.RData | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 12:34:58 28-08-12 |
| Completed: | 12:48:50 28-08-12 |
| Elapsed: | 00 hrs 13 mins 52 secs |
