| ClinicalAnalysisAllGenes_new1 data file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/PANCANCER/1457187/0.GDAC_mRNA_Preprocess_Median.Finished/PANCANCER.medianexp.txt |
| ClinicalAnalysisAllGenes_new1 clinical file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/PANCANCER/1445490/1.GDAC_clinicalDataPicker.Finished/PANCANCER.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 | MRNA_EXPR |
| Execution Times: | |
| Submitted: | 18:09:36 19-07-12 |
| Completed: | |
| Elapsed: | 01 hrs 32 mins 06 secs |
step 1. ClinicalAnalysisAllGenes_new [id: 132495] 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:00333:11
| data file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/PANCANCER/1457187/0.GDAC_mRNA_Preprocess_Median.Finished/PANCANCER.medianexp.txt |
| clinical file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/PANCANCER/1445490/1.GDAC_clinicalDataPicker.Finished/PANCANCER.clin.merged.picked.txt |
| genes filtered by list | |
| genes filtered by variance | ALL |
| samples filtered by list | |
| features used | ALL |
| output name | |
| job description |
| Output Files: | |
| PANCANCER.clin.merged.picked.clindata.txt | |
| PANCANCER.medianexp.exprdata.gct | |
| PANCANCER.medianexp.clinical.results.txt | |
| PANCANCER.medianexp.analysis.results.RData | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 18:09:37 19-07-12 |
| Completed: | 19:41:10 19-07-12 |
| Elapsed: | 01 hrs 31 mins 33 secs |
step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 132496] Generate a report to summarize the results from ClinicalAnalysisAllGenes module
urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:20
| all result file | PANCANCER.medianexp.clinical.results.txt |
| RData file | PANCANCER.medianexp.analysis.results.RData |
| expression file | PANCANCER.medianexp.exprdata.gct |
| clinical file | PANCANCER.clin.merged.picked.clindata.txt |
| cutoff p | 1 |
| cutoff fdr | 0.05 |
| max table rows | 10 |
| nozzle ver | Nozzle.R1 |
| options | MRNA_EXPR |
| report title | |
| job description |
| Execution Times: | |
| Submitted: | 18:09:37 19-07-12 |
| Completed: | 19:41:41 19-07-12 |
| Elapsed: | 01 hrs 32 mins 04 secs |