| GDAC_TopgenesforCluster1 expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PANCANCER/1445235/2.GDAC_MergeDataFiles.Finished/PANCANCER.mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.txt |
| GDAC_TopgenesforCluster1 selectedgenes | 150 |
| GDAC_NmfConsensusClustering2 k int | 2 |
| GDAC_NmfConsensusClustering2 k final | 8 |
| GDAC_CNMFselectcluster3 output | PANCANCER |
| GDAC_CNMFselectcluster3 inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PANCANCER/1445235/2.GDAC_MergeDataFiles.Finished/PANCANCER.mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.txt |
| GDAC_CnmfReports4 report | mirna |
| Execution Times: | |
| Submitted: | 19:40:42 25-07-12 |
| Completed: | |
| Elapsed: | 03 hrs 52 mins 24 secs |
step 1. GDAC_TopgenesforCluster [id: 137070] 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_MergeDataFilesPipeline/PANCANCER/1445235/2.GDAC_MergeDataFiles.Finished/PANCANCER.mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.txt |
| selectedgenes | 150 |
| outputprefix | outputprefix |
| Output Files: | |
| .lsf.out | |
| outputprefix.expclu.gct | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 19:40:42 25-07-12 |
| Completed: | 19:41:38 25-07-12 |
| Elapsed: | 00 hrs 00 mins 55 secs |
step 2. GDAC_NmfConsensusClustering [id: 137071] 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: | 19:40:42 25-07-12 |
| Completed: | 23:32:03 25-07-12 |
| Elapsed: | 03 hrs 51 mins 21 secs |
step 3. GDAC_CNMFselectcluster [id: 137072] selecte best cluster
urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:27
| measure | Pearson |
| inputexp | outputprefix.expclu.gct |
| clumembership | cnmf.membership.txt |
| output | PANCANCER |
| inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PANCANCER/1445235/2.GDAC_MergeDataFiles.Finished/PANCANCER.mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.txt |
| cophenetic | cnmf.cophenetic.coefficient.txt |
| Execution Times: | |
| Submitted: | 19:40:42 25-07-12 |
| Completed: | 23:32:50 25-07-12 |
| Elapsed: | 03 hrs 52 mins 07 secs |
step 4. GDAC_CnmfReports [id: 137073]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:19
| kclus | PANCANCER.silfig.png |
| markers | PANCANCER.selectedSubclassmarkers.txt |
| bestclu | PANCANCER.bestclus.txt |
| allcluster | cnmf.membership.txt |
| cormatrix | PANCANCER.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 | PANCANCER.selectedSubclassmarkers.txt |
| heatmap | PANCANCER.geneheatmap.png |
| heatmapall | PANCANCER.geneheatmaptopgenes.png |
| report | mirna |
| Output Files: | |
| nozzle.html | |
| .lsf.out | |
| nozzle.RData | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 19:40:42 25-07-12 |
| Completed: | 23:33:05 25-07-12 |
| Elapsed: | 03 hrs 52 mins 22 secs |
