| GDAC_TopgenesforCluster1 expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/BRCA/1456393/0.GDAC_MethylationPreprocess.Finished/BRCA.meth.filtered.txt |
| GDAC_TopgenesforCluster1 selectedgenes | 8547 |
| 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/GDAC_MethylationPreprocess/BRCA/1456393/0.GDAC_MethylationPreprocess.Finished/BRCA.meth.filtered.txt |
| GDAC_CnmfReports4 report | methylation |
| Execution Times: | |
| Submitted: | 19:42:04 25-07-12 |
| Completed: | |
| Elapsed: | 10 hrs 48 mins 56 secs |
step 1. GDAC_TopgenesforCluster [id: 137147] 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/GDAC_MethylationPreprocess/BRCA/1456393/0.GDAC_MethylationPreprocess.Finished/BRCA.meth.filtered.txt |
| selectedgenes | 8547 |
| outputprefix | outputprefix |
| Output Files: | |
| outputprefix.expclu.gct | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 19:42:04 25-07-12 |
| Completed: | 20:26:56 25-07-12 |
| Elapsed: | 00 hrs 44 mins 52 secs |
step 2. GDAC_NmfConsensusClustering [id: 137148] 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: | 19:42:04 25-07-12 |
| Completed: | 05:53:21 26-07-12 |
| Elapsed: | 10 hrs 11 mins 17 secs |
step 3. GDAC_CNMFselectcluster [id: 137149] selecte best cluster
urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:27
| measure | Pearson |
| inputexp | outputprefix.expclu.gct |
| clumembership | cnmf.membership.txt |
| output | BRCA |
| inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/BRCA/1456393/0.GDAC_MethylationPreprocess.Finished/BRCA.meth.filtered.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 | |
| BRCA.geneheatmaptopgenes.png | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 19:42:04 25-07-12 |
| Completed: | 06:30:30 26-07-12 |
| Elapsed: | 10 hrs 48 mins 25 secs |
step 4. GDAC_CnmfReports [id: 137150]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:19
| 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 | methylation |
| Output Files: | |
| nozzle.html | |
| .lsf.out | |
| nozzle.RData | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 19:42:04 25-07-12 |
| Completed: | 06:30:59 26-07-12 |
| Elapsed: | 10 hrs 48 mins 54 secs |
