GDAC_TopgenesforCluster1 expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/miRseq_mature_preprocess/KIRC-TP/3471887/KIRC-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 | KIRC-TP |
GDAC_selectBestcluster3 inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/miRseq_mature_preprocess/KIRC-TP/3471887/KIRC-TP.miRseq_mature_PKM_log2.txt |
GDAC_CnmfReports4 report | hclumiRseqMature |
Execution Times: | |
Submitted: | 10:50:11 06-06-13 |
Completed: | |
Elapsed: | 00 hrs 15 mins 32 secs |
step 1. GDAC_TopgenesforCluster [id: 416550] 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/KIRC-TP/3471887/KIRC-TP.miRseq_mature_PKM_log2.txt |
selectedgenes | 0.25 |
outputprefix | outputprefix |
Output Files: | |
.lsf.out | |
outputprefix.expclu.gct | |
stdout.txt |
Execution Times: | |
Submitted: | 10:50:14 06-06-13 |
Completed: | 11:03:31 06-06-13 |
Elapsed: | 00 hrs 13 mins 16 secs |
step 2. GDAC_ConsensusClustering [id: 416551] 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: | 10:50:14 06-06-13 |
Completed: | 11:04:35 06-06-13 |
Elapsed: | 00 hrs 14 mins 20 secs |
step 3. GDAC_selectBestcluster [id: 416552]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00207:32
measure | Pearson |
inputexp | outputprefix.expclu.gct |
output | KIRC-TP |
file clu 2 | outputprefix.expclu.sub173.2.clu |
file clu 3 | outputprefix.expclu.sub173.3.clu |
file clu 4 | outputprefix.expclu.sub173.4.clu |
file clu 5 | outputprefix.expclu.sub173.5.clu |
file clu 6 | outputprefix.expclu.sub173.6.clu |
file clu 7 | outputprefix.expclu.sub173.7.clu |
file clu 8 | outputprefix.expclu.sub173.8.clu |
inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/miRseq_mature_preprocess/KIRC-TP/3471887/KIRC-TP.miRseq_mature_PKM_log2.txt |
Execution Times: | |
Submitted: | 10:50:14 06-06-13 |
Completed: | 11:05:14 06-06-13 |
Elapsed: | 00 hrs 15 mins 00 secs |
step 4. GDAC_CnmfReports [id: 416553]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:23
kclus | KIRC-TP.silfig.png |
markers | KIRC-TP.subclassmarkers.txt |
bestclu | KIRC-TP.bestclus.txt |
allcluster | KIRC-TP.allclusters.txt |
cormatrix | KIRC-TP.cormatrix.png |
file gif 2 | outputprefix.expclu.sub173.srt.2.gif |
file gif 3 | outputprefix.expclu.sub173.srt.3.gif |
file gif 4 | outputprefix.expclu.sub173.srt.4.gif |
file gif 5 | outputprefix.expclu.sub173.srt.5.gif |
file gif 6 | outputprefix.expclu.sub173.srt.6.gif |
file gif 7 | outputprefix.expclu.sub173.srt.7.gif |
file gif 8 | outputprefix.expclu.sub173.srt.8.gif |
expdata | outputprefix.expclu.gct |
markersP | KIRC-TP.seclectedSubclassmarkers.txt |
heatmap | KIRC-TP.geneheatmap.png |
heatmapall | KIRC-TP.geneheatmaptopgenes.png |
report | hclumiRseqMature |
Output Files: | |
nozzle.html | |
.lsf.out | |
nozzle.RData | |
stdout.txt |
Execution Times: | |
Submitted: | 10:50:14 06-06-13 |
Completed: | 11:05:42 06-06-13 |
Elapsed: | 00 hrs 15 mins 27 secs |