GDAC_TopgenesforCluster1 expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/LAML-TB/3026140/LAML-TB.uncv2.mRNAseq_RSEM_normalized_log2.txt |
GDAC_TopgenesforCluster1 selectedgenes | 1500 |
GDAC_NmfConsensusClustering2 k int | 2 |
GDAC_NmfConsensusClustering2 k final | 10 |
GDAC_CNMFselectcluster3 output | LAML-TB |
GDAC_CNMFselectcluster3 inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/LAML-TB/3026140/LAML-TB.uncv2.mRNAseq_RSEM_normalized_log2.txt |
GDAC_CnmfReports4 report | mRNAseq |
Execution Times: | |
Submitted: | 13:52:32 02-05-13 |
Completed: | |
Elapsed: | 00 hrs 23 mins 26 secs |
step 1. GDAC_TopgenesforCluster [id: 395384] 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/LAML-TB/3026140/LAML-TB.uncv2.mRNAseq_RSEM_normalized_log2.txt |
selectedgenes | 1500 |
outputprefix | outputprefix |
Output Files: | |
.lsf.out | |
outputprefix.expclu.gct | |
stdout.txt |
Execution Times: | |
Submitted: | 13:52:32 02-05-13 |
Completed: | 13:54:23 02-05-13 |
Elapsed: | 00 hrs 01 mins 50 secs |
step 2. GDAC_NmfConsensusClustering [id: 395385] 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: | 13:52:32 02-05-13 |
Completed: | 14:12:48 02-05-13 |
Elapsed: | 00 hrs 20 mins 16 secs |
step 3. GDAC_CNMFselectcluster [id: 395386] selecte best cluster
urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:39
measure | Pearson |
inputexp | outputprefix.expclu.gct |
clumembership | cnmf.membership.txt |
output | LAML-TB |
inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/LAML-TB/3026140/LAML-TB.uncv2.mRNAseq_RSEM_normalized_log2.txt |
cophenetic | cnmf.cophenetic.coefficient.txt |
Execution Times: | |
Submitted: | 13:52:32 02-05-13 |
Completed: | 14:15:39 02-05-13 |
Elapsed: | 00 hrs 23 mins 06 secs |
step 4. GDAC_CnmfReports [id: 395387]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:22
kclus | LAML-TB.silfig.png |
markers | LAML-TB.subclassmarkers.txt |
bestclu | LAML-TB.bestclus.txt |
allcluster | cnmf.membership.txt |
cormatrix | LAML-TB.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 | LAML-TB.selectmarker.txt |
heatmap | LAML-TB.geneheatmap.png |
heatmapall | LAML-TB.geneheatmaptopgenes.png |
report | mRNAseq |
Output Files: | |
nozzle.html | |
.lsf.out | |
nozzle.RData | |
stdout.txt |
Execution Times: | |
Submitted: | 13:52:32 02-05-13 |
Completed: | 14:15:57 02-05-13 |
Elapsed: | 00 hrs 23 mins 24 secs |