GDAC_TopgenesforCluster1 expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/COADREAD-TP/2843419/COADREAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt |
GDAC_TopgenesforCluster1 selectedgenes | 1500 |
GDAC_NmfConsensusClustering2 k int | 2 |
GDAC_NmfConsensusClustering2 k final | 10 |
GDAC_CNMFselectcluster3 output | COADREAD-TP |
GDAC_CNMFselectcluster3 inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/COADREAD-TP/2843419/COADREAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt |
GDAC_CnmfReports4 report | mRNAseq |
Execution Times: | |
Submitted: | 18:52:24 08-04-13 |
Completed: | |
Elapsed: | 06 hrs 44 mins 22 secs |
step 1. GDAC_TopgenesforCluster [id: 372943] 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/mRNAseq_preprocessor/COADREAD-TP/2843419/COADREAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt |
selectedgenes | 1500 |
outputprefix | outputprefix |
Output Files: | |
outputprefix.expclu.gct | |
.lsf.out | |
stdout.txt |
Execution Times: | |
Submitted: | 18:52:32 08-04-13 |
Completed: | 22:12:28 08-04-13 |
Elapsed: | 03 hrs 19 mins 55 secs |
step 2. GDAC_NmfConsensusClustering [id: 372944] 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: | 18:52:32 08-04-13 |
Completed: | 00:49:08 09-04-13 |
Elapsed: | 05 hrs 56 mins 35 secs |
step 3. GDAC_CNMFselectcluster [id: 372945] selecte best cluster
urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:39
measure | Pearson |
inputexp | outputprefix.expclu.gct |
clumembership | cnmf.membership.txt |
output | COADREAD-TP |
inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/COADREAD-TP/2843419/COADREAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt |
cophenetic | cnmf.cophenetic.coefficient.txt |
Execution Times: | |
Submitted: | 18:52:32 08-04-13 |
Completed: | 01:36:17 09-04-13 |
Elapsed: | 06 hrs 43 mins 44 secs |
step 4. GDAC_CnmfReports [id: 372946]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:22
kclus | COADREAD-TP.silfig.png |
markers | COADREAD-TP.subclassmarkers.txt |
bestclu | COADREAD-TP.bestclus.txt |
allcluster | cnmf.membership.txt |
cormatrix | COADREAD-TP.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 | COADREAD-TP.selectmarker.txt |
heatmap | COADREAD-TP.geneheatmap.png |
heatmapall | COADREAD-TP.geneheatmaptopgenes.png |
report | mRNAseq |
Output Files: | |
nozzle.html | |
.lsf.out | |
nozzle.RData | |
stdout.txt |
Execution Times: | |
Submitted: | 18:52:32 08-04-13 |
Completed: | 01:36:45 09-04-13 |
Elapsed: | 06 hrs 44 mins 12 secs |