| GDAC_TopgenesforCluster1 expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/LUAD-TP/2600659/0.mRNAseq_preprocessor.Finished/LUAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt |
| GDAC_TopgenesforCluster1 selectedgenes | 1500 |
| GDAC_ConsensusClustering2 clustering algorithm | HIERARCHICAL |
| GDAC_ConsensusClustering2 cluster by | |
| GDAC_ConsensusClustering2 distance measure | PEARSON |
| GDAC_ConsensusClustering2 normalize type | -n2 |
| GDAC_selectBestcluster3 measure | Pearson |
| GDAC_selectBestcluster3 output | LUAD-TP |
| GDAC_selectBestcluster3 inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/LUAD-TP/2600659/0.mRNAseq_preprocessor.Finished/LUAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt |
| GDAC_CnmfReports4 report | hclumRNAseq |
| Execution Times: | |
| Submitted: | 15:17:52 04-03-13 |
| Completed: | |
| Elapsed: | 00 hrs 10 mins 10 secs |
step 1. GDAC_TopgenesforCluster [id: 333608] 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/mRNAseq_preprocessor/LUAD-TP/2600659/0.mRNAseq_preprocessor.Finished/LUAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt |
| selectedgenes | 1500 |
| outputprefix | outputprefix |
| Output Files: | |
| outputprefix.expclu.gct | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 15:17:55 04-03-13 |
| Completed: | 15:21:29 04-03-13 |
| Elapsed: | 00 hrs 03 mins 34 secs |
step 2. GDAC_ConsensusClustering [id: 333609] Resampling-based clustering method
urn:lsid:broadinstitute.org:cancer.genome.analysis:00158:6
| input filename | outputprefix.expclu.gct |
| kmax | 8 |
| resampling iterations | 20 |
| seed value | 12345 |
| clustering algorithm | HIERARCHICAL |
| cluster by | |
| distance measure | PEARSON |
| resample | subsample |
| merge type | average |
| descent iterations | 2000 |
| output stub | <input.filename_basename> |
| normalize type | -n2 |
| normalization iterations | 0 |
| create heat map | -p |
| heat map size | 2 |
| Execution Times: | |
| Submitted: | 15:17:55 04-03-13 |
| Completed: | 15:24:28 04-03-13 |
| Elapsed: | 00 hrs 06 mins 33 secs |
step 3. GDAC_selectBestcluster [id: 333610]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00207:32
| measure | Pearson |
| inputexp | outputprefix.expclu.gct |
| output | LUAD-TP |
| file clu 2 | outputprefix.expclu.sub282.2.clu |
| file clu 3 | outputprefix.expclu.sub282.3.clu |
| file clu 4 | outputprefix.expclu.sub282.4.clu |
| file clu 5 | outputprefix.expclu.sub282.5.clu |
| file clu 6 | outputprefix.expclu.sub282.6.clu |
| file clu 7 | outputprefix.expclu.sub282.7.clu |
| file clu 8 | outputprefix.expclu.sub282.8.clu |
| inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/LUAD-TP/2600659/0.mRNAseq_preprocessor.Finished/LUAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt |
| Execution Times: | |
| Submitted: | 15:17:55 04-03-13 |
| Completed: | 15:27:49 04-03-13 |
| Elapsed: | 00 hrs 09 mins 54 secs |
step 4. GDAC_CnmfReports [id: 333611]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:21
| kclus | LUAD-TP.silfig.png |
| markers | LUAD-TP.subclassmarkers.txt |
| bestclu | LUAD-TP.bestclus.txt |
| allcluster | LUAD-TP.allclusters.txt |
| cormatrix | LUAD-TP.cormatrix.png |
| file gif 2 | outputprefix.expclu.sub282.srt.2.gif |
| file gif 3 | outputprefix.expclu.sub282.srt.3.gif |
| file gif 4 | outputprefix.expclu.sub282.srt.4.gif |
| file gif 5 | outputprefix.expclu.sub282.srt.5.gif |
| file gif 6 | outputprefix.expclu.sub282.srt.6.gif |
| file gif 7 | outputprefix.expclu.sub282.srt.7.gif |
| file gif 8 | outputprefix.expclu.sub282.srt.8.gif |
| expdata | outputprefix.expclu.gct |
| markersP | LUAD-TP.seclectedSubclassmarkers.txt |
| heatmap | LUAD-TP.geneheatmap.png |
| heatmapall | LUAD-TP.geneheatmaptopgenes.png |
| report | hclumRNAseq |
| Output Files: | |
| nozzle.RData | |
| nozzle.html | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 15:17:55 04-03-13 |
| Completed: | 15:28:01 04-03-13 |
| Elapsed: | 00 hrs 10 mins 06 secs |
