| ClinicalAnalysisAllGenes_new1 data file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/COADREAD/1676551/0.GDAC_mRNA_Preprocess_Median.Finished/COADREAD.medianexp.txt |
| ClinicalAnalysisAllGenes_new1 clinical file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/COADREAD/1669311/1.GDAC_clinicalDataPicker.Finished/COADREAD.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: | 17:11:26 18-09-12 |
| Completed: | |
| Elapsed: | 00 hrs 13 mins 26 secs |
step 1. ClinicalAnalysisAllGenes_new [id: 169361] 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/GDAC_mRNA_Preprocess_Median/COADREAD/1676551/0.GDAC_mRNA_Preprocess_Median.Finished/COADREAD.medianexp.txt |
| clinical file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/COADREAD/1669311/1.GDAC_clinicalDataPicker.Finished/COADREAD.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: | |
| COADREAD.clin.merged.picked.clindata.txt | |
| COADREAD.medianexp.exprdata.gct | |
| COADREAD.medianexp.analysis.results.RData | |
| COADREAD.medianexp.clinical.results.txt | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 17:11:26 18-09-12 |
| Completed: | 17:24:19 18-09-12 |
| Elapsed: | 00 hrs 12 mins 53 secs |
step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 169362] Generate a report to summarize the results from ClinicalAnalysisAllGenes module
urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:29
| all result file | COADREAD.medianexp.clinical.results.txt |
| RData file | COADREAD.medianexp.analysis.results.RData |
| expression file | COADREAD.medianexp.exprdata.gct |
| clinical file | COADREAD.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: | 17:11:26 18-09-12 |
| Completed: | 17:24:52 18-09-12 |
| Elapsed: | 00 hrs 13 mins 25 secs |