| GDAC_TopgenesforCluster1 expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/COADREAD/1311028/0.mRNAseq_preprocessor.Finished/COADREAD.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 | COADREAD |
| GDAC_selectBestcluster3 inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/COADREAD/1311028/0.mRNAseq_preprocessor.Finished/COADREAD.mRNAseq_RPKM_tmm_log2.txt |
| GDAC_CnmfReports4 report | hclumRNAseq |
| Execution Times: | |
| Submitted: | 06:19:18 10-06-12 |
| Completed: | |
| Elapsed: | 00 hrs 09 mins 27 secs |
step 1. GDAC_TopgenesforCluster [id: 110618] 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/COADREAD/1311028/0.mRNAseq_preprocessor.Finished/COADREAD.mRNAseq_RPKM_tmm_log2.txt |
| selectedgenes | 1500 |
| outputprefix | outputprefix |
| Output Files: | |
| outputprefix.expclu.gct | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 06:19:20 10-06-12 |
| Completed: | 06:21:46 10-06-12 |
| Elapsed: | 00 hrs 02 mins 26 secs |
step 2. GDAC_ConsensusClustering [id: 110619] 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: | 06:19:20 10-06-12 |
| Completed: | 06:25:20 10-06-12 |
| Elapsed: | 00 hrs 05 mins 59 secs |
step 3. GDAC_selectBestcluster [id: 110620]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00207:29
| measure | Pearson |
| inputexp | outputprefix.expclu.gct |
| output | COADREAD |
| file clu 2 | outputprefix.expclu.sub66.2.clu |
| file clu 3 | outputprefix.expclu.sub66.3.clu |
| file clu 4 | outputprefix.expclu.sub66.4.clu |
| file clu 5 | outputprefix.expclu.sub66.5.clu |
| file clu 6 | outputprefix.expclu.sub66.6.clu |
| file clu 7 | outputprefix.expclu.sub66.7.clu |
| file clu 8 | outputprefix.expclu.sub66.8.clu |
| inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/COADREAD/1311028/0.mRNAseq_preprocessor.Finished/COADREAD.mRNAseq_RPKM_tmm_log2.txt |
| Execution Times: | |
| Submitted: | 06:19:20 10-06-12 |
| Completed: | 06:27:55 10-06-12 |
| Elapsed: | 00 hrs 08 mins 35 secs |
step 4. GDAC_CnmfReports [id: 110621]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:10
| kclus | COADREAD.silfig.png |
| markers | COADREAD.subclassmarkers.txt |
| bestclu | COADREAD.bestclus.txt |
| allcluster | COADREAD.allclusters.txt |
| cormatrix | COADREAD.cormatrix.png |
| file gif 2 | outputprefix.expclu.sub66.srt.2.gif |
| file gif 3 | outputprefix.expclu.sub66.srt.3.gif |
| file gif 4 | outputprefix.expclu.sub66.srt.4.gif |
| file gif 5 | outputprefix.expclu.sub66.srt.5.gif |
| file gif 6 | outputprefix.expclu.sub66.srt.6.gif |
| file gif 7 | outputprefix.expclu.sub66.srt.7.gif |
| file gif 8 | outputprefix.expclu.sub66.srt.8.gif |
| expdata | outputprefix.expclu.gct |
| markersP | COADREAD.seclectedSubclassmarkers.txt |
| heatmap | COADREAD.geneheatmap.png |
| heatmapall | COADREAD.geneheatmaptopgenes.png |
| report | hclumRNAseq |
| Output Files: | |
| nozzle.RData | |
| nozzle.html | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 06:19:20 10-06-12 |
| Completed: | 06:28:44 10-06-12 |
| Elapsed: | 00 hrs 09 mins 24 secs |
