GDAC_TopgenesforCluster1 expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/LUSC-TP/2624464/0.mRNAseq_preprocessor.Finished/LUSC-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 | LUSC-TP |
GDAC_selectBestcluster3 inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/LUSC-TP/2624464/0.mRNAseq_preprocessor.Finished/LUSC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt |
GDAC_CnmfReports4 report | hclumRNAseq |
Execution Times: | |
Submitted: | 15:29:31 04-03-13 |
Completed: | |
Elapsed: | 00 hrs 06 mins 47 secs |
step 1. GDAC_TopgenesforCluster [id: 333741] 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/LUSC-TP/2624464/0.mRNAseq_preprocessor.Finished/LUSC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt |
selectedgenes | 1500 |
outputprefix | outputprefix |
Output Files: | |
outputprefix.expclu.gct | |
.lsf.out | |
stdout.txt |
Execution Times: | |
Submitted: | 15:29:31 04-03-13 |
Completed: | 15:32:07 04-03-13 |
Elapsed: | 00 hrs 02 mins 35 secs |
step 2. GDAC_ConsensusClustering [id: 333742] 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: | 15:29:31 04-03-13 |
Completed: | 15:33:12 04-03-13 |
Elapsed: | 00 hrs 03 mins 41 secs |
step 3. GDAC_selectBestcluster [id: 333743]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00207:32
measure | Pearson |
inputexp | outputprefix.expclu.gct |
output | LUSC-TP |
file clu 2 | outputprefix.expclu.sub206.2.clu |
file clu 3 | outputprefix.expclu.sub206.3.clu |
file clu 4 | outputprefix.expclu.sub206.4.clu |
file clu 5 | outputprefix.expclu.sub206.5.clu |
file clu 6 | outputprefix.expclu.sub206.6.clu |
file clu 7 | outputprefix.expclu.sub206.7.clu |
file clu 8 | outputprefix.expclu.sub206.8.clu |
inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/LUSC-TP/2624464/0.mRNAseq_preprocessor.Finished/LUSC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt |
Execution Times: | |
Submitted: | 15:29:31 04-03-13 |
Completed: | 15:36:02 04-03-13 |
Elapsed: | 00 hrs 06 mins 30 secs |
step 4. GDAC_CnmfReports [id: 333744]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:21
kclus | LUSC-TP.silfig.png |
markers | LUSC-TP.seclectedSubclassmarkers.txt |
bestclu | LUSC-TP.bestclus.txt |
allcluster | LUSC-TP.allclusters.txt |
cormatrix | LUSC-TP.cormatrix.png |
file gif 2 | outputprefix.expclu.sub206.srt.2.gif |
file gif 3 | outputprefix.expclu.sub206.srt.3.gif |
file gif 4 | outputprefix.expclu.sub206.srt.4.gif |
file gif 5 | outputprefix.expclu.sub206.srt.5.gif |
file gif 6 | outputprefix.expclu.sub206.srt.6.gif |
file gif 7 | outputprefix.expclu.sub206.srt.7.gif |
file gif 8 | outputprefix.expclu.sub206.srt.8.gif |
expdata | outputprefix.expclu.gct |
markersP | LUSC-TP.seclectedSubclassmarkers.txt |
heatmap | LUSC-TP.geneheatmap.png |
heatmapall | LUSC-TP.geneheatmaptopgenes.png |
report | hclumRNAseq |
Output Files: | |
nozzle.RData | |
nozzle.html | |
.lsf.out | |
stdout.txt |
Execution Times: | |
Submitted: | 15:29:31 04-03-13 |
Completed: | 15:36:17 04-03-13 |
Elapsed: | 00 hrs 06 mins 46 secs |