GDAC_TopgenesforCluster1 expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/miRseq_mature_preprocess/BLCA-TP/3471803/BLCA-TP.miRseq_mature_PKM_log2.txt |
GDAC_TopgenesforCluster1 selectedgenes | 0.25 |
GDAC_ConsensusClustering2 clustering algorithm | HIERARCHICAL |
GDAC_ConsensusClustering2 cluster by | |
GDAC_ConsensusClustering2 distance measure | PEARSON |
GDAC_ConsensusClustering2 normalize type | |
GDAC_selectBestcluster3 measure | Pearson |
GDAC_selectBestcluster3 output | BLCA-TP |
GDAC_selectBestcluster3 inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/miRseq_mature_preprocess/BLCA-TP/3471803/BLCA-TP.miRseq_mature_PKM_log2.txt |
GDAC_CnmfReports4 report | hclumiRseqMature |
Execution Times: | |
Submitted: | 10:49:01 06-06-13 |
Completed: | |
Elapsed: | 00 hrs 12 mins 24 secs |
step 1. GDAC_TopgenesforCluster [id: 416349] 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:00205:36
expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/miRseq_mature_preprocess/BLCA-TP/3471803/BLCA-TP.miRseq_mature_PKM_log2.txt |
selectedgenes | 0.25 |
outputprefix | outputprefix |
Output Files: | |
.lsf.out | |
outputprefix.expclu.gct | |
stdout.txt |
Execution Times: | |
Submitted: | 10:49:06 06-06-13 |
Completed: | 10:55:05 06-06-13 |
Elapsed: | 00 hrs 05 mins 59 secs |
step 2. GDAC_ConsensusClustering [id: 416352] 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 | |
normalization iterations | 0 |
create heat map | -p |
heat map size | 2 |
Execution Times: | |
Submitted: | 10:49:06 06-06-13 |
Completed: | 10:57:54 06-06-13 |
Elapsed: | 00 hrs 08 mins 47 secs |
step 3. GDAC_selectBestcluster [id: 416354]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00207:32
measure | Pearson |
inputexp | outputprefix.expclu.gct |
output | BLCA-TP |
file clu 2 | outputprefix.expclu.sub122.2.clu |
file clu 3 | outputprefix.expclu.sub122.3.clu |
file clu 4 | outputprefix.expclu.sub122.4.clu |
file clu 5 | outputprefix.expclu.sub122.5.clu |
file clu 6 | outputprefix.expclu.sub122.6.clu |
file clu 7 | outputprefix.expclu.sub122.7.clu |
file clu 8 | outputprefix.expclu.sub122.8.clu |
inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/miRseq_mature_preprocess/BLCA-TP/3471803/BLCA-TP.miRseq_mature_PKM_log2.txt |
Execution Times: | |
Submitted: | 10:49:06 06-06-13 |
Completed: | 10:59:59 06-06-13 |
Elapsed: | 00 hrs 10 mins 52 secs |
step 4. GDAC_CnmfReports [id: 416356]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:23
kclus | BLCA-TP.silfig.png |
markers | BLCA-TP.seclectedSubclassmarkers.txt |
bestclu | BLCA-TP.bestclus.txt |
allcluster | BLCA-TP.allclusters.txt |
cormatrix | BLCA-TP.cormatrix.png |
file gif 2 | outputprefix.expclu.sub122.srt.2.gif |
file gif 3 | outputprefix.expclu.sub122.srt.3.gif |
file gif 4 | outputprefix.expclu.sub122.srt.4.gif |
file gif 5 | outputprefix.expclu.sub122.srt.5.gif |
file gif 6 | outputprefix.expclu.sub122.srt.6.gif |
file gif 7 | outputprefix.expclu.sub122.srt.7.gif |
file gif 8 | outputprefix.expclu.sub122.srt.8.gif |
expdata | outputprefix.expclu.gct |
markersP | BLCA-TP.seclectedSubclassmarkers.txt |
heatmap | BLCA-TP.geneheatmap.png |
heatmapall | BLCA-TP.geneheatmaptopgenes.png |
report | hclumiRseqMature |
Output Files: | |
nozzle.html | |
.lsf.out | |
nozzle.RData | |
stdout.txt |
Execution Times: | |
Submitted: | 10:49:06 06-06-13 |
Completed: | 11:01:23 06-06-13 |
Elapsed: | 00 hrs 12 mins 16 secs |