GDAC_TopgenesforCluster1 expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/SKCM-TM/3141126/0.GDAC_MethylationPreprocess.Finished/SKCM-TM.meth.for_clustering.filtered_data.txt |
GDAC_TopgenesforCluster1 selectedgenes | 11014 |
GDAC_NmfConsensusClustering2 k int | 2 |
GDAC_NmfConsensusClustering2 k final | 8 |
GDAC_CNMFselectcluster3 output | SKCM-TM |
GDAC_CNMFselectcluster3 inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/SKCM-TM/3141126/0.GDAC_MethylationPreprocess.Finished/SKCM-TM.meth.for_clustering.filtered_data.txt |
GDAC_CnmfReports4 report | methylation |
Execution Times: | |
Submitted: | 15:14:12 02-05-13 |
Completed: | |
Elapsed: | 05 hrs 01 mins 55 secs |
step 1. GDAC_TopgenesforCluster [id: 396766] 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/SKCM-TM/3141126/0.GDAC_MethylationPreprocess.Finished/SKCM-TM.meth.for_clustering.filtered_data.txt |
selectedgenes | 11014 |
outputprefix | outputprefix |
Output Files: | |
.lsf.out | |
outputprefix.expclu.gct | |
stdout.txt |
Execution Times: | |
Submitted: | 15:14:18 02-05-13 |
Completed: | 15:46:56 02-05-13 |
Elapsed: | 00 hrs 32 mins 37 secs |
step 2. GDAC_NmfConsensusClustering [id: 396767] 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: | 15:14:18 02-05-13 |
Completed: | 19:11:55 02-05-13 |
Elapsed: | 03 hrs 57 mins 36 secs |
step 3. GDAC_CNMFselectcluster [id: 396768] selecte best cluster
urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:39
measure | Pearson |
inputexp | outputprefix.expclu.gct |
clumembership | cnmf.membership.txt |
output | SKCM-TM |
inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/SKCM-TM/3141126/0.GDAC_MethylationPreprocess.Finished/SKCM-TM.meth.for_clustering.filtered_data.txt |
cophenetic | cnmf.cophenetic.coefficient.txt |
Execution Times: | |
Submitted: | 15:14:18 02-05-13 |
Completed: | 20:15:50 02-05-13 |
Elapsed: | 05 hrs 01 mins 31 secs |
step 4. GDAC_CnmfReports [id: 396769]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:22
kclus | SKCM-TM.silfig.png |
markers | SKCM-TM.subclassmarkers.txt |
bestclu | SKCM-TM.bestclus.txt |
allcluster | cnmf.membership.txt |
cormatrix | SKCM-TM.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 | SKCM-TM.selectmarker.txt |
heatmap | SKCM-TM.geneheatmap.png |
heatmapall | SKCM-TM.geneheatmaptopgenes.png |
report | methylation |
Output Files: | |
nozzle.RData | |
nozzle.html | |
.lsf.out | |
stdout.txt |
Execution Times: | |
Submitted: | 15:14:18 02-05-13 |
Completed: | 20:16:05 02-05-13 |
Elapsed: | 05 hrs 01 mins 47 secs |