| GDAC_TopgenesforCluster1 expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BRCA/1676449/0.mRNAseq_preprocessor.Finished/BRCA.uncv2.mRNAseq_RSEM_normalized_log2.txt |
| GDAC_TopgenesforCluster1 selectedgenes | 1500 |
| GDAC_ConsensusClustering2 clustering algorithm | HIERARCHICAL |
| GDAC_ConsensusClustering2 cluster by | |
| GDAC_ConsensusClustering2 distance measure | PEARSON |
| GDAC_ConsensusClustering2 normalize type | -n2 |
| GDAC_selectBestcluster3 measure | Pearson |
| GDAC_selectBestcluster3 output | BRCA |
| GDAC_selectBestcluster3 inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BRCA/1676449/0.mRNAseq_preprocessor.Finished/BRCA.uncv2.mRNAseq_RSEM_normalized_log2.txt |
| GDAC_CnmfReports4 report | hclumRNAseq |
| Execution Times: | |
| Submitted: | 11:21:29 28-08-12 |
| Completed: | |
| Elapsed: | 01 hrs 05 mins 39 secs |
step 1. GDAC_TopgenesforCluster [id: 157516] 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:00205:29
| expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BRCA/1676449/0.mRNAseq_preprocessor.Finished/BRCA.uncv2.mRNAseq_RSEM_normalized_log2.txt |
| selectedgenes | 1500 |
| outputprefix | outputprefix |
| Output Files: | |
| outputprefix.expclu.gct | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 11:21:29 28-08-12 |
| Completed: | 11:30:28 28-08-12 |
| Elapsed: | 00 hrs 08 mins 58 secs |
step 2. GDAC_ConsensusClustering [id: 157517] 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 | -n2 |
| normalization iterations | 0 |
| create heat map | -p |
| heat map size | 2 |
| Execution Times: | |
| Submitted: | 11:21:29 28-08-12 |
| Completed: | 12:20:10 28-08-12 |
| Elapsed: | 00 hrs 58 mins 40 secs |
step 3. GDAC_selectBestcluster [id: 157518]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00207:32
| measure | Pearson |
| inputexp | outputprefix.expclu.gct |
| output | BRCA |
| file clu 2 | outputprefix.expclu.sub644.2.clu |
| file clu 3 | outputprefix.expclu.sub644.3.clu |
| file clu 4 | outputprefix.expclu.sub644.4.clu |
| file clu 5 | outputprefix.expclu.sub644.5.clu |
| file clu 6 | outputprefix.expclu.sub644.6.clu |
| file clu 7 | outputprefix.expclu.sub644.7.clu |
| file clu 8 | outputprefix.expclu.sub644.8.clu |
| inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BRCA/1676449/0.mRNAseq_preprocessor.Finished/BRCA.uncv2.mRNAseq_RSEM_normalized_log2.txt |
| Execution Times: | |
| Submitted: | 11:21:29 28-08-12 |
| Completed: | 12:26:38 28-08-12 |
| Elapsed: | 01 hrs 05 mins 08 secs |
step 4. GDAC_CnmfReports [id: 157519]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:21
| kclus | BRCA.silfig.png |
| markers | BRCA.subclassmarkers.txt |
| bestclu | BRCA.bestclus.txt |
| allcluster | BRCA.allclusters.txt |
| cormatrix | BRCA.cormatrix.png |
| file gif 2 | outputprefix.expclu.sub644.srt.2.gif |
| file gif 3 | outputprefix.expclu.sub644.srt.3.gif |
| file gif 4 | outputprefix.expclu.sub644.srt.4.gif |
| file gif 5 | outputprefix.expclu.sub644.srt.5.gif |
| file gif 6 | outputprefix.expclu.sub644.srt.6.gif |
| file gif 7 | outputprefix.expclu.sub644.srt.7.gif |
| file gif 8 | outputprefix.expclu.sub644.srt.8.gif |
| expdata | outputprefix.expclu.gct |
| markersP | BRCA.seclectedSubclassmarkers.txt |
| heatmap | BRCA.geneheatmap.png |
| heatmapall | BRCA.geneheatmaptopgenes.png |
| report | hclumRNAseq |
| Output Files: | |
| nozzle.RData | |
| nozzle.html | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 11:21:29 28-08-12 |
| Completed: | 12:27:07 28-08-12 |
| Elapsed: | 01 hrs 05 mins 37 secs |
