GDAC_TopgenesforCluster1 expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/GBM/2008380/0.mRNAseq_preprocessor.Finished/GBM.uncv2.mRNAseq_RSEM_normalized_log2.txt |
GDAC_TopgenesforCluster1 selectedgenes | 1500 |
GDAC_NmfConsensusClustering2 k int | 2 |
GDAC_NmfConsensusClustering2 k final | 10 |
GDAC_CNMFselectcluster3 output | GBM |
GDAC_CNMFselectcluster3 inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/GBM/2008380/0.mRNAseq_preprocessor.Finished/GBM.uncv2.mRNAseq_RSEM_normalized_log2.txt |
GDAC_CnmfReports4 report | mRNAseq |
Execution Times: | |
Submitted: | 12:54:50 08-11-12 |
Completed: | |
Elapsed: | 00 hrs 25 mins 17 secs |
step 1. GDAC_TopgenesforCluster [id: 222569] 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:00205:33
expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/GBM/2008380/0.mRNAseq_preprocessor.Finished/GBM.uncv2.mRNAseq_RSEM_normalized_log2.txt |
selectedgenes | 1500 |
outputprefix | outputprefix |
Output Files: | |
outputprefix.expclu.gct | |
.lsf.out | |
stdout.txt |
Execution Times: | |
Submitted: | 12:54:58 08-11-12 |
Completed: | 12:57:18 08-11-12 |
Elapsed: | 00 hrs 02 mins 19 secs |
step 2. GDAC_NmfConsensusClustering [id: 222570] 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 | 10 |
outputprefix | cnmf |
Execution Times: | |
Submitted: | 12:54:58 08-11-12 |
Completed: | 13:13:54 08-11-12 |
Elapsed: | 00 hrs 18 mins 55 secs |
step 3. GDAC_CNMFselectcluster [id: 222571] selecte best cluster
urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:33
measure | Pearson |
inputexp | outputprefix.expclu.gct |
clumembership | cnmf.membership.txt |
output | GBM |
inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/GBM/2008380/0.mRNAseq_preprocessor.Finished/GBM.uncv2.mRNAseq_RSEM_normalized_log2.txt |
cophenetic | cnmf.cophenetic.coefficient.txt |
Output Files: | |
GBM.bestclus.txt | |
GBM.silfig.png | |
GBM.cormatrix.png | |
GBM.subclassmarkers.txt | |
GBM.selectmarker.txt | |
GBM.geneheatmap.png | |
GBM.geneheatmaptopgenes.png | |
.lsf.out | |
stdout.txt |
Execution Times: | |
Submitted: | 12:54:58 08-11-12 |
Completed: | 13:18:39 08-11-12 |
Elapsed: | 00 hrs 23 mins 40 secs |
step 4. GDAC_CnmfReports [id: 222572]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:22
kclus | GBM.silfig.png |
markers | GBM.subclassmarkers.txt |
bestclu | GBM.bestclus.txt |
allcluster | cnmf.membership.txt |
cormatrix | GBM.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 | GBM.selectmarker.txt |
heatmap | GBM.geneheatmap.png |
heatmapall | GBM.geneheatmaptopgenes.png |
report | mRNAseq |
Output Files: | |
nozzle.html | |
nozzle.RData | |
.lsf.out | |
stdout.txt |
Execution Times: | |
Submitted: | 12:54:58 08-11-12 |
Completed: | 13:20:06 08-11-12 |
Elapsed: | 00 hrs 25 mins 07 secs |