| GDAC_TopgenesforCluster1 expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/CN_preprocess/BLCA-TP/6155986/BLCA-TP.cn_focal_gistic_thrshold.txt |
| GDAC_TopgenesforCluster1 selectedgenes | ALL |
| GDAC_NmfConsensusClustering2 k int | 2 |
| GDAC_NmfConsensusClustering2 k final | 8 |
| GDAC_CNMFselectcluster3 output | BLCA-TP |
| GDAC_CNMFselectcluster3 inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/CN_preprocess/BLCA-TP/6155986/BLCA-TP.cn_focal_gistic.txt |
| GDAC_CnmfReports4 report | nmfCNT |
| Execution Times: | |
| Submitted: | 22:52:28 26-01-14 |
| Completed: | |
| Elapsed: | 00 hrs 13 mins 39 secs |
step 1. GDAC_TopgenesforCluster [id: 502661] 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/BLCA-TP/6155986/BLCA-TP.cn_focal_gistic_thrshold.txt |
| selectedgenes | ALL |
| outputprefix | outputprefix |
| Output Files: | |
| .lsf.out | |
| outputprefix.expclu.gct | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 22:52:28 26-01-14 |
| Completed: | 22:53:55 26-01-14 |
| Elapsed: | 00 hrs 01 mins 26 secs |
step 2. GDAC_NmfConsensusClustering [id: 502662] 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: | 22:52:28 26-01-14 |
| Completed: | 23:02:03 26-01-14 |
| Elapsed: | 00 hrs 09 mins 34 secs |
step 3. GDAC_CNMFselectcluster [id: 502663] selecte best cluster
urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:45
| measure | Pearson |
| inputexp | outputprefix.expclu.gct |
| clumembership | cnmf.membership.txt |
| output | BLCA-TP |
| inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/CN_preprocess/BLCA-TP/6155986/BLCA-TP.cn_focal_gistic.txt |
| cophenetic | cnmf.cophenetic.coefficient.txt |
| Execution Times: | |
| Submitted: | 22:52:28 26-01-14 |
| Completed: | 23:02:18 26-01-14 |
| Elapsed: | 00 hrs 09 mins 49 secs |
step 4. GDAC_CnmfReports [id: 502664]
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| kclus | BLCA-TP.silfig.png |
| markers | BLCA-TP.subclassmarkers.txt |
| bestclu | BLCA-TP.bestclus.txt |
| allcluster | cnmf.membership.txt |
| cormatrix | BLCA-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 | BLCA-TP.selectmarker.txt |
| heatmap | BLCA-TP.geneheatmap.png |
| heatmapall | BLCA-TP.geneheatmaptopgenes.png |
| report | nmfCNT |
| Output Files: | |
| nozzle.html | |
| nozzle.RData | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 22:52:28 26-01-14 |
| Completed: | 23:06:06 26-01-14 |
| Elapsed: | 00 hrs 13 mins 38 secs |
