| GDAC_TopgenesforCluster1 expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/COAD/2008292/0.GDAC_mRNA_Preprocess_Median.Finished/COAD.medianexp.txt |
| GDAC_TopgenesforCluster1 selectedgenes | 1500 |
| GDAC_NmfConsensusClustering2 k int | 2 |
| GDAC_NmfConsensusClustering2 k final | 8 |
| GDAC_CNMFselectcluster3 output | COAD |
| GDAC_CNMFselectcluster3 inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/COAD/2008292/0.GDAC_mRNA_Preprocess_Median.Finished/COAD.medianexp.txt |
| GDAC_CnmfReports4 report | mrna |
| Execution Times: | |
| Submitted: | 12:47:01 08-11-12 |
| Completed: | |
| Elapsed: | 00 hrs 25 mins 58 secs |
step 1. GDAC_TopgenesforCluster [id: 222309] 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:00205:33
| expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/COAD/2008292/0.GDAC_mRNA_Preprocess_Median.Finished/COAD.medianexp.txt |
| selectedgenes | 1500 |
| outputprefix | outputprefix |
| Output Files: | |
| outputprefix.expclu.gct | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 12:47:14 08-11-12 |
| Completed: | 12:49:31 08-11-12 |
| Elapsed: | 00 hrs 02 mins 16 secs |
step 2. GDAC_NmfConsensusClustering [id: 222310] Non-negative Matrix Factorization (NMF) Consensus Clustering, http://www.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=89
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| expfile | outputprefix.expclu.gct |
| k int | 2 |
| k final | 8 |
| outputprefix | cnmf |
| Execution Times: | |
| Submitted: | 12:47:14 08-11-12 |
| Completed: | 13:05:55 08-11-12 |
| Elapsed: | 00 hrs 18 mins 41 secs |
step 3. GDAC_CNMFselectcluster [id: 222311] selecte best cluster
urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:33
| measure | Pearson |
| inputexp | outputprefix.expclu.gct |
| clumembership | cnmf.membership.txt |
| output | COAD |
| inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/COAD/2008292/0.GDAC_mRNA_Preprocess_Median.Finished/COAD.medianexp.txt |
| cophenetic | cnmf.cophenetic.coefficient.txt |
| Output Files: | |
| COAD.bestclus.txt | |
| COAD.cormatrix.png | |
| COAD.silfig.png | |
| COAD.subclassmarkers.txt | |
| COAD.selectmarker.txt | |
| COAD.geneheatmap.png | |
| COAD.geneheatmaptopgenes.png | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 12:47:14 08-11-12 |
| Completed: | 13:10:48 08-11-12 |
| Elapsed: | 00 hrs 23 mins 33 secs |
step 4. GDAC_CnmfReports [id: 222312]
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| kclus | COAD.silfig.png |
| markers | COAD.subclassmarkers.txt |
| bestclu | COAD.bestclus.txt |
| allcluster | cnmf.membership.txt |
| cormatrix | COAD.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 | COAD.selectmarker.txt |
| heatmap | COAD.geneheatmap.png |
| heatmapall | COAD.geneheatmaptopgenes.png |
| report | mrna |
| Output Files: | |
| nozzle.RData | |
| nozzle.html | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 12:47:14 08-11-12 |
| Completed: | 13:12:58 08-11-12 |
| Elapsed: | 00 hrs 25 mins 43 secs |
