GDAC_TopgenesforCluster1 expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/BLCA/2016696/0.GDAC_MethylationPreprocess.Finished/BLCA.meth.for_clustering.filtered_data.txt |
GDAC_TopgenesforCluster1 selectedgenes | 10059 |
GDAC_NmfConsensusClustering2 k int | 2 |
GDAC_NmfConsensusClustering2 k final | 8 |
GDAC_CNMFselectcluster3 output | BLCA |
GDAC_CNMFselectcluster3 inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/BLCA/2016696/0.GDAC_MethylationPreprocess.Finished/BLCA.meth.for_clustering.filtered_data.txt |
GDAC_CnmfReports4 report | methylation |
Execution Times: | |
Submitted: | 17:37:08 09-11-12 |
Completed: | |
Elapsed: | 04 hrs 06 mins 09 secs |
step 1. GDAC_TopgenesforCluster [id: 226574] 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:00205:35
expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/BLCA/2016696/0.GDAC_MethylationPreprocess.Finished/BLCA.meth.for_clustering.filtered_data.txt |
selectedgenes | 10059 |
outputprefix | outputprefix |
Output Files: | |
.lsf.out | |
outputprefix.expclu.gct | |
stdout.txt |
Execution Times: | |
Submitted: | 17:37:08 09-11-12 |
Completed: | 18:40:49 09-11-12 |
Elapsed: | 01 hrs 03 mins 41 secs |
step 2. GDAC_NmfConsensusClustering [id: 226575] Non-negative Matrix Factorization (NMF) Consensus Clustering, http://www.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=89
urn:lsid:broadinstitute.org:cancer.genome.analysis:00379:39
expfile | outputprefix.expclu.gct |
k int | 2 |
k final | 8 |
outputprefix | cnmf |
Execution Times: | |
Submitted: | 17:37:08 09-11-12 |
Completed: | 20:42:33 09-11-12 |
Elapsed: | 03 hrs 05 mins 25 secs |
step 3. GDAC_CNMFselectcluster [id: 226576] selecte best cluster
urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:35
measure | Pearson |
inputexp | outputprefix.expclu.gct |
clumembership | cnmf.membership.txt |
output | BLCA |
inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/BLCA/2016696/0.GDAC_MethylationPreprocess.Finished/BLCA.meth.for_clustering.filtered_data.txt |
cophenetic | cnmf.cophenetic.coefficient.txt |
Output Files: | |
BLCA.silfig.png | |
BLCA.cormatrix.png | |
BLCA.bestclus.txt | |
BLCA.selectmarker.txt | |
BLCA.subclassmarkers.txt | |
BLCA.geneheatmap.png | |
BLCA.geneheatmaptopgenes.png | |
.lsf.out | |
stdout.txt |
Execution Times: | |
Submitted: | 17:37:08 09-11-12 |
Completed: | 21:43:01 09-11-12 |
Elapsed: | 04 hrs 05 mins 52 secs |
step 4. GDAC_CnmfReports [id: 226577]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:22
kclus | BLCA.silfig.png |
markers | BLCA.subclassmarkers.txt |
bestclu | BLCA.bestclus.txt |
allcluster | cnmf.membership.txt |
cormatrix | BLCA.cormatrix.png |
file gif 2 | cnmf.consensus.plot.k2.png |
file gif 3 | cnmf.consensus.plot.k3.png |
file gif 4 | cnmf.consensus.plot.k4.png |
file gif 5 | cnmf.consensus.plot.k5.png |
file gif 6 | cnmf.consensus.plot.k6.png |
file gif 7 | cnmf.consensus.plot.k7.png |
file gif 8 | cnmf.consensus.plot.k8.png |
expdata | outputprefix.expclu.gct |
markersP | BLCA.selectmarker.txt |
heatmap | BLCA.geneheatmap.png |
heatmapall | BLCA.geneheatmaptopgenes.png |
report | methylation |
Output Files: | |
nozzle.html | |
nozzle.RData | |
.lsf.out | |
stdout.txt |
Execution Times: | |
Submitted: | 17:37:08 09-11-12 |
Completed: | 21:43:16 09-11-12 |
Elapsed: | 04 hrs 06 mins 07 secs |