| GDAC_TopgenesforCluster1 expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/CN_preprocess/BRCA-TP/6158666/BRCA-TP.cn_focal_gistic_thrshold.txt |
| GDAC_TopgenesforCluster1 selectedgenes | ALL |
| GDAC_NmfConsensusClustering2 k int | 2 |
| GDAC_NmfConsensusClustering2 k final | 8 |
| GDAC_CNMFselectcluster3 output | BRCA-TP |
| GDAC_CNMFselectcluster3 inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/CN_preprocess/BRCA-TP/6158666/BRCA-TP.cn_focal_gistic.txt |
| GDAC_CnmfReports4 report | nmfCNT |
| Execution Times: | |
| Submitted: | 03:37:44 27-01-14 |
| Completed: | |
| Elapsed: | 15 hrs 06 mins 57 secs |
step 1. GDAC_TopgenesforCluster [id: 503309] 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:00205:36
| expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/CN_preprocess/BRCA-TP/6158666/BRCA-TP.cn_focal_gistic_thrshold.txt |
| selectedgenes | ALL |
| outputprefix | outputprefix |
| Output Files: | |
| .lsf.out | |
| outputprefix.expclu.gct | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 03:37:44 27-01-14 |
| Completed: | 03:37:59 27-01-14 |
| Elapsed: | 00 hrs 00 mins 14 secs |
step 2. GDAC_NmfConsensusClustering [id: 503310] 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: | 03:37:44 27-01-14 |
| Completed: | 18:43:10 28-01-14 |
| Elapsed: | 15 hrs 05 mins 25 secs |
step 3. GDAC_CNMFselectcluster [id: 503311] selecte best cluster
urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:45
| measure | Pearson |
| inputexp | outputprefix.expclu.gct |
| clumembership | cnmf.membership.txt |
| output | BRCA-TP |
| inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/CN_preprocess/BRCA-TP/6158666/BRCA-TP.cn_focal_gistic.txt |
| cophenetic | cnmf.cophenetic.coefficient.txt |
| Execution Times: | |
| Submitted: | 03:37:44 27-01-14 |
| Completed: | 18:44:14 28-01-14 |
| Elapsed: | 15 hrs 06 mins 29 secs |
step 4. GDAC_CnmfReports [id: 503312]
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| kclus | BRCA-TP.silfig.png |
| markers | BRCA-TP.subclassmarkers.txt |
| bestclu | BRCA-TP.bestclus.txt |
| allcluster | cnmf.membership.txt |
| cormatrix | BRCA-TP.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-TP.selectmarker.txt |
| heatmap | BRCA-TP.geneheatmap.png |
| heatmapall | BRCA-TP.geneheatmaptopgenes.png |
| report | nmfCNT |
| Output Files: | |
| nozzle.RData | |
| nozzle.html | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 03:37:44 27-01-14 |
| Completed: | 18:44:40 28-01-14 |
| Elapsed: | 15 hrs 06 mins 56 secs |
