| ClinicalAnalysisAllGenes_new1 data file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/SKCM/1768862/0.mRNAseq_preprocessor.Finished/SKCM.uncv2.mRNAseq_RSEM_normalized_log2.txt |
| ClinicalAnalysisAllGenes_new1 clinical file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/SKCM/1709388/1.GDAC_clinicalDataPicker.Finished/SKCM.clin.merged.picked.txt |
| ClinicalAnalysisAllGenesReport_nozzle2 cutoff p | 1 |
| ClinicalAnalysisAllGenesReport_nozzle2 cutoff fdr | 0.05 |
| ClinicalAnalysisAllGenesReport_nozzle2 max table rows | 10 |
| ClinicalAnalysisAllGenesReport_nozzle2 nozzle ver | Nozzle.R1 |
| ClinicalAnalysisAllGenesReport_nozzle2 options | MRNASEQ_EXPR |
| Execution Times: | |
| Submitted: | 05:21:21 04-10-12 |
| Completed: | |
| Elapsed: | 00 hrs 11 mins 04 secs |
step 1. ClinicalAnalysisAllGenes_new [id: 176147] Associate individual gene expression profiles to clinical parameters by survival test, t-test, correlation test, or ANOVA test
urn:lsid:broadinstitute.org:cancer.genome.analysis:00333:13
| data file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/SKCM/1768862/0.mRNAseq_preprocessor.Finished/SKCM.uncv2.mRNAseq_RSEM_normalized_log2.txt |
| clinical file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/SKCM/1709388/1.GDAC_clinicalDataPicker.Finished/SKCM.clin.merged.picked.txt |
| genes filtered by list | |
| genes filtered by variance | ALL |
| samples filtered by list | |
| features used | ALL |
| output name | |
| job description |
| Execution Times: | |
| Submitted: | 05:21:53 04-10-12 |
| Completed: | 05:30:03 04-10-12 |
| Elapsed: | 00 hrs 08 mins 09 secs |
step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 176148] Generate a report to summarize the results from ClinicalAnalysisAllGenes module
urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:29
| all result file | SKCM.uncv2.mRNAseq_RSEM_normalized_log2.clinical.results.txt |
| RData file | SKCM.uncv2.mRNAseq_RSEM_normalized_log2.analysis.results.RData |
| expression file | SKCM.uncv2.mRNAseq_RSEM_normalized_log2.exprdata.gct |
| clinical file | SKCM.clin.merged.picked.clindata.txt |
| cutoff p | 1 |
| cutoff fdr | 0.05 |
| max table rows | 10 |
| nozzle ver | Nozzle.R1 |
| options | MRNASEQ_EXPR |
| report title | |
| job description |
| Output Files: | |
| table1.txt | |
| supp.table1.txt | |
| V3ex.png | |
| nozzle.html | |
| table5.txt | |
| .lsf.out | |
| nozzle.RData | |
| V3ex.pdf | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 05:21:53 04-10-12 |
| Completed: | 05:32:24 04-10-12 |
| Elapsed: | 00 hrs 10 mins 31 secs |