| GDAC_TopgenesforCluster1 expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/STAD/868756/0.mRNAseq_preprocessor.Finished/STAD.mRNAseq_RPKM_tmm_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 | STAD |
| GDAC_selectBestcluster3 inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/STAD/868756/0.mRNAseq_preprocessor.Finished/STAD.mRNAseq_RPKM_tmm_log2.txt |
| GDAC_CnmfReports4 report | hclumRNAseq |
| Execution Times: | |
| Submitted: | 11:40:19 28-02-12 |
| Completed: | |
| Elapsed: | 00 hrs 04 mins 36 secs |
step 1. GDAC_TopgenesforCluster [id: 57520] 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:00205:19
| expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/STAD/868756/0.mRNAseq_preprocessor.Finished/STAD.mRNAseq_RPKM_tmm_log2.txt |
| selectedgenes | 1500 |
| outputprefix | outputprefix |
| Output Files: | |
| outputprefix.expclu.gct | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 11:40:19 28-02-12 |
| Completed: | 11:41:22 28-02-12 |
| Elapsed: | 00 hrs 01 mins 02 secs |
step 2. GDAC_ConsensusClustering [id: 57521] 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: | 11:40:19 28-02-12 |
| Completed: | 11:41:49 28-02-12 |
| Elapsed: | 00 hrs 01 mins 29 secs |
step 3. GDAC_selectBestcluster [id: 57522]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00207:29
| measure | Pearson |
| inputexp | outputprefix.expclu.gct |
| output | STAD |
| file clu 2 | outputprefix.expclu.sub46.2.clu |
| file clu 3 | outputprefix.expclu.sub46.3.clu |
| file clu 4 | outputprefix.expclu.sub46.4.clu |
| file clu 5 | outputprefix.expclu.sub46.5.clu |
| file clu 6 | outputprefix.expclu.sub46.6.clu |
| file clu 7 | outputprefix.expclu.sub46.7.clu |
| file clu 8 | outputprefix.expclu.sub46.8.clu |
| inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/STAD/868756/0.mRNAseq_preprocessor.Finished/STAD.mRNAseq_RPKM_tmm_log2.txt |
| Execution Times: | |
| Submitted: | 11:40:19 28-02-12 |
| Completed: | 11:44:02 28-02-12 |
| Elapsed: | 00 hrs 03 mins 43 secs |
step 4. GDAC_CnmfReports [id: 57523]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:10
| kclus | STAD.silfig.png |
| markers | STAD.subclassmarkers.txt |
| bestclu | STAD.bestclus.txt |
| allcluster | STAD.allclusters.txt |
| cormatrix | STAD.cormatrix.png |
| file gif 2 | outputprefix.expclu.sub46.srt.2.gif |
| file gif 3 | outputprefix.expclu.sub46.srt.3.gif |
| file gif 4 | outputprefix.expclu.sub46.srt.4.gif |
| file gif 5 | outputprefix.expclu.sub46.srt.5.gif |
| file gif 6 | outputprefix.expclu.sub46.srt.6.gif |
| file gif 7 | outputprefix.expclu.sub46.srt.7.gif |
| file gif 8 | outputprefix.expclu.sub46.srt.8.gif |
| expdata | outputprefix.expclu.gct |
| markersP | STAD.seclectedSubclassmarkers.txt |
| heatmap | STAD.geneheatmap.png |
| heatmapall | STAD.geneheatmaptopgenes.png |
| report | hclumRNAseq |
| Output Files: | |
| nozzle.html | |
| .lsf.out | |
| nozzle.RData | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 11:40:19 28-02-12 |
| Completed: | 11:44:54 28-02-12 |
| Elapsed: | 00 hrs 04 mins 34 secs |
