| GDAC_TopgenesforCluster1 expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BRCA/1311023/0.mRNAseq_preprocessor.Finished/BRCA.mRNAseq_RPKM_tmm_log2.txt |
| GDAC_TopgenesforCluster1 selectedgenes | 1500 |
| 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/mRNAseq_preprocessor/BRCA/1311023/0.mRNAseq_preprocessor.Finished/BRCA.mRNAseq_RPKM_tmm_log2.txt |
| GDAC_CnmfReports4 report | mRNAseq |
| Execution Times: | |
| Submitted: | 06:19:13 10-06-12 |
| Completed: | |
| Elapsed: | 22 hrs 50 mins 30 secs |
step 1. GDAC_TopgenesforCluster [id: 110606] 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:00205:20
| expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BRCA/1311023/0.mRNAseq_preprocessor.Finished/BRCA.mRNAseq_RPKM_tmm_log2.txt |
| selectedgenes | 1500 |
| outputprefix | outputprefix |
| Output Files: | |
| outputprefix.expclu.gct | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 06:19:19 10-06-12 |
| Completed: | 06:32:11 10-06-12 |
| Elapsed: | 00 hrs 12 mins 52 secs |
step 2. GDAC_NmfConsensusClustering [id: 110607] 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:00379:38
| expfile | outputprefix.expclu.gct |
| k int | 2 |
| k final | 8 |
| outputprefix | cnmf |
| Execution Times: | |
| Submitted: | 06:19:19 10-06-12 |
| Completed: | 05:00:25 11-06-12 |
| Elapsed: | 22 hrs 41 mins 06 secs |
step 3. GDAC_CNMFselectcluster [id: 110608] selecte best cluster
urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:24
| measure | Pearson |
| inputexp | outputprefix.expclu.gct |
| clumembership | cnmf.membership.txt |
| output | BRCA |
| inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BRCA/1311023/0.mRNAseq_preprocessor.Finished/BRCA.mRNAseq_RPKM_tmm_log2.txt |
| cophenetic | cnmf.cophenetic.coefficient.txt |
| Output Files: | |
| BRCA.silfig.png | |
| BRCA.cormatrix.png | |
| BRCA.bestclus.txt | |
| BRCA.subclassmarkers.txt | |
| BRCA.seclectedSubclassmarkers.txt | |
| BRCA.geneheatmap.png | |
| BRCA.geneheatmaptopgenes.png | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 06:19:19 10-06-12 |
| Completed: | 05:09:27 11-06-12 |
| Elapsed: | 22 hrs 50 mins 08 secs |
step 4. GDAC_CnmfReports [id: 110609]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:10
| kclus | BRCA.silfig.png |
| markers | BRCA.subclassmarkers.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.seclectedSubclassmarkers.txt |
| heatmap | BRCA.geneheatmap.png |
| heatmapall | BRCA.geneheatmaptopgenes.png |
| report | mRNAseq |
| Output Files: | |
| nozzle.html | |
| .lsf.out | |
| nozzle.RData | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 06:19:19 10-06-12 |
| Completed: | 05:09:42 11-06-12 |
| Elapsed: | 22 hrs 50 mins 23 secs |
