GDAC_TopgenesforCluster1 expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/KIRP/1590232/0.GDAC_mRNA_Preprocess_Median.Finished/KIRP.medianexp.txt |
GDAC_TopgenesforCluster1 selectedgenes | 1500 |
GDAC_NmfConsensusClustering2 k int | 2 |
GDAC_NmfConsensusClustering2 k final | 8 |
GDAC_CNMFselectcluster3 output | KIRP |
GDAC_CNMFselectcluster3 inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/KIRP/1590232/0.GDAC_mRNA_Preprocess_Median.Finished/KIRP.medianexp.txt |
GDAC_CnmfReports4 report | mrna |
Execution Times: | |
Submitted: | 17:58:06 01-08-12 |
Completed: | |
Elapsed: | 00 hrs 32 mins 04 secs |
step 1. GDAC_TopgenesforCluster [id: 140712] 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:00205:29
expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/KIRP/1590232/0.GDAC_mRNA_Preprocess_Median.Finished/KIRP.medianexp.txt |
selectedgenes | 1500 |
outputprefix | outputprefix |
Output Files: | |
.lsf.out | |
outputprefix.expclu.gct | |
stdout.txt |
Execution Times: | |
Submitted: | 17:58:07 01-08-12 |
Completed: | 17:59:29 01-08-12 |
Elapsed: | 00 hrs 01 mins 22 secs |
step 2. GDAC_NmfConsensusClustering [id: 140713] 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: | 17:58:07 01-08-12 |
Completed: | 18:28:52 01-08-12 |
Elapsed: | 00 hrs 30 mins 45 secs |
step 3. GDAC_CNMFselectcluster [id: 140714] selecte best cluster
urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:27
measure | Pearson |
inputexp | outputprefix.expclu.gct |
clumembership | cnmf.membership.txt |
output | KIRP |
inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/KIRP/1590232/0.GDAC_mRNA_Preprocess_Median.Finished/KIRP.medianexp.txt |
cophenetic | cnmf.cophenetic.coefficient.txt |
Output Files: | |
KIRP.cormatrix.png | |
KIRP.silfig.png | |
KIRP.bestclus.txt | |
KIRP.geneheatmap.png | |
KIRP.subclassmarkers.txt | |
KIRP.selectedSubclassmarkers.txt | |
KIRP.geneheatmaptopgenes.png | |
.lsf.out | |
stdout.txt |
Execution Times: | |
Submitted: | 17:58:07 01-08-12 |
Completed: | 18:29:37 01-08-12 |
Elapsed: | 00 hrs 31 mins 30 secs |
step 4. GDAC_CnmfReports [id: 140715]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:19
kclus | KIRP.silfig.png |
markers | KIRP.subclassmarkers.txt |
bestclu | KIRP.bestclus.txt |
allcluster | cnmf.membership.txt |
cormatrix | KIRP.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 | KIRP.selectedSubclassmarkers.txt |
heatmap | KIRP.geneheatmap.png |
heatmapall | KIRP.geneheatmaptopgenes.png |
report | mrna |
Output Files: | |
nozzle.html | |
.lsf.out | |
nozzle.RData | |
stdout.txt |
Execution Times: | |
Submitted: | 17:58:07 01-08-12 |
Completed: | 18:30:09 01-08-12 |
Elapsed: | 00 hrs 32 mins 02 secs |