GDAC_TopgenesforCluster1 expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/miRseq_preprocessor/OV/689508/0.miRseq_preprocessor.Finished/OV.miRseq_RPKM_tmm_log2.txt |
GDAC_TopgenesforCluster1 selectedgenes | 150 |
GDAC_NmfConsensusClustering2 k int | 2 |
GDAC_NmfConsensusClustering2 k final | 8 |
GDAC_CNMFselectcluster3 output | OV |
GDAC_CNMFselectcluster3 inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/miRseq_preprocessor/OV/689508/0.miRseq_preprocessor.Finished/OV.miRseq_RPKM_tmm_log2.txt |
GDAC_CnmfReports4 report | miRseq |
Execution Times: | |
Submitted: | 02:38:20 02-03-12 |
Completed: | |
Elapsed: | 00 hrs 05 mins 26 secs |
step 1. GDAC_TopgenesforCluster [id: 58789] 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:00205:19
expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/miRseq_preprocessor/OV/689508/0.miRseq_preprocessor.Finished/OV.miRseq_RPKM_tmm_log2.txt |
selectedgenes | 150 |
outputprefix | outputprefix |
Output Files: | |
outputprefix.expclu.gct | |
stdout.txt |
Execution Times: | |
Submitted: | 02:38:20 02-03-12 |
Completed: | 02:38:33 02-03-12 |
Elapsed: | 00 hrs 00 mins 13 secs |
step 2. GDAC_NmfConsensusClustering [id: 58790] 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:00379:37
expfile | outputprefix.expclu.gct |
k int | 2 |
k final | 8 |
outputprefix | cnmf |
Execution Times: | |
Submitted: | 02:38:20 02-03-12 |
Completed: | 02:41:35 02-03-12 |
Elapsed: | 00 hrs 03 mins 14 secs |
step 3. GDAC_CNMFselectcluster [id: 58791] selecte best cluster
urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:24
measure | Pearson |
inputexp | outputprefix.expclu.gct |
clumembership | cnmf.membership.txt |
output | OV |
inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/miRseq_preprocessor/OV/689508/0.miRseq_preprocessor.Finished/OV.miRseq_RPKM_tmm_log2.txt |
cophenetic | cnmf.cophenetic.coefficient.txt |
Output Files: | |
OV.cormatrix.png | |
OV.silfig.png | |
OV.bestclus.txt | |
OV.subclassmarkers.txt | |
OV.seclectedSubclassmarkers.txt | |
OV.geneheatmap.png | |
OV.geneheatmaptopgenes.png | |
.lsf.out | |
stdout.txt |
Execution Times: | |
Submitted: | 02:38:20 02-03-12 |
Completed: | 02:42:22 02-03-12 |
Elapsed: | 00 hrs 04 mins 02 secs |
step 4. GDAC_CnmfReports [id: 58792]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:10
kclus | OV.silfig.png |
markers | OV.subclassmarkers.txt |
bestclu | OV.bestclus.txt |
allcluster | cnmf.membership.txt |
cormatrix | OV.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 | OV.seclectedSubclassmarkers.txt |
heatmap | OV.geneheatmap.png |
heatmapall | OV.geneheatmaptopgenes.png |
report | miRseq |
Output Files: | |
nozzle.RData | |
nozzle.html | |
.lsf.out | |
stdout.txt |
Execution Times: | |
Submitted: | 02:38:20 02-03-12 |
Completed: | 02:43:43 02-03-12 |
Elapsed: | 00 hrs 05 mins 22 secs |