| GDAC_TopgenesforCluster1 expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/CN_preprocess/BRCA/1684433/0.CN_preprocess.Finished/BRCA.cn_focal_gistic.txt |
| GDAC_TopgenesforCluster1 selectedgenes | ALL |
| GDAC_NmfConsensusClustering2 k int | 2 |
| GDAC_NmfConsensusClustering2 k final | 8 |
| GDAC_CNMFselectcluster3 output | BRCA |
| GDAC_CNMFselectcluster3 inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/CN_preprocess/BRCA/1684433/0.CN_preprocess.Finished/BRCA.cn_focal_gistic.txt |
| GDAC_CnmfReports4 report | nmfCN |
| Execution Times: | |
| Submitted: | 16:44:51 31-08-12 |
| Completed: | |
| Elapsed: | 05 hrs 07 mins 32 secs |
step 1. GDAC_TopgenesforCluster [id: 161079] 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:00205:33
| expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/CN_preprocess/BRCA/1684433/0.CN_preprocess.Finished/BRCA.cn_focal_gistic.txt |
| selectedgenes | ALL |
| outputprefix | outputprefix |
| Output Files: | |
| .lsf.out | |
| outputprefix.expclu.gct | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 16:44:51 31-08-12 |
| Completed: | 16:45:16 31-08-12 |
| Elapsed: | 00 hrs 00 mins 24 secs |
step 2. GDAC_NmfConsensusClustering [id: 161080] Non-negative Matrix Factorization (NMF) Consensus Clustering, http://www.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=89
urn:lsid:broadinstitute.org:cancer.genome.analysis:00379:39
| expfile | outputprefix.expclu.gct |
| k int | 2 |
| k final | 8 |
| outputprefix | cnmf |
| Execution Times: | |
| Submitted: | 16:44:51 31-08-12 |
| Completed: | 21:49:18 01-09-12 |
| Elapsed: | 05 hrs 04 mins 26 secs |
step 3. GDAC_CNMFselectcluster [id: 161081] selecte best cluster
urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:31
| measure | Pearson |
| inputexp | outputprefix.expclu.gct |
| clumembership | cnmf.membership.txt |
| output | BRCA |
| inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/CN_preprocess/BRCA/1684433/0.CN_preprocess.Finished/BRCA.cn_focal_gistic.txt |
| cophenetic | cnmf.cophenetic.coefficient.txt |
| Output Files: | |
| BRCA.silfig.png | |
| BRCA.cormatrix.png | |
| BRCA.bestclus.txt | |
| BRCA.selectedSubclassmarkers.txt | |
| BRCA.subclassmarkers.txt | |
| BRCA.geneheatmap.png | |
| .lsf.out | |
| BRCA.geneheatmaptopgenes.png | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 16:44:52 31-08-12 |
| Completed: | 21:50:06 01-09-12 |
| Elapsed: | 05 hrs 05 mins 14 secs |
step 4. GDAC_CnmfReports [id: 161082]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:22
| kclus | BRCA.silfig.png |
| markers | BRCA.selectedSubclassmarkers.txt |
| bestclu | BRCA.bestclus.txt |
| allcluster | cnmf.membership.txt |
| cormatrix | BRCA.cormatrix.png |
| file gif 2 | cnmf.consensus.plot.k2.png |
| file gif 3 | cnmf.consensus.plot.k3.png |
| file gif 4 | cnmf.consensus.plot.k4.png |
| file gif 5 | cnmf.consensus.plot.k5.png |
| file gif 6 | cnmf.consensus.plot.k6.png |
| file gif 7 | cnmf.consensus.plot.k7.png |
| file gif 8 | cnmf.consensus.plot.k8.png |
| expdata | outputprefix.expclu.gct |
| markersP | BRCA.selectedSubclassmarkers.txt |
| heatmap | BRCA.geneheatmap.png |
| heatmapall | BRCA.geneheatmaptopgenes.png |
| report | nmfCN |
| Output Files: | |
| nozzle.html | |
| .lsf.out | |
| nozzle.RData | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 16:44:52 31-08-12 |
| Completed: | 21:52:21 01-09-12 |
| Elapsed: | 05 hrs 07 mins 29 secs |
