| ClinicalAnalysisAllGenes_new1 data file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/COAD-TP/2356709/0.GDAC_mRNA_Preprocess_Median.Finished/COAD-TP.medianexp.txt |
| ClinicalAnalysisAllGenes_new1 clinical file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/COAD-TP/2330183/1.GDAC_clinicalDataPicker.Finished/COAD-TP.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: | 15:55:05 29-01-13 |
| Completed: | |
| Elapsed: | 00 hrs 10 mins 22 secs |
step 1. ClinicalAnalysisAllGenes_new [id: 300661] 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/COAD-TP/2356709/0.GDAC_mRNA_Preprocess_Median.Finished/COAD-TP.medianexp.txt |
| clinical file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/COAD-TP/2330183/1.GDAC_clinicalDataPicker.Finished/COAD-TP.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: | |
| COAD-TP.clin.merged.picked.clindata.txt | |
| COAD-TP.medianexp.exprdata.gct | |
| COAD-TP.medianexp.analysis.results.RData | |
| COAD-TP.medianexp.clinical.results.txt | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 15:55:09 29-01-13 |
| Completed: | 16:04:49 29-01-13 |
| Elapsed: | 00 hrs 09 mins 39 secs |
step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 300662] Generate a report to summarize the results from ClinicalAnalysisAllGenes module
urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:29
| all result file | COAD-TP.medianexp.clinical.results.txt |
| RData file | COAD-TP.medianexp.analysis.results.RData |
| expression file | COAD-TP.medianexp.exprdata.gct |
| clinical file | COAD-TP.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: | 15:55:09 29-01-13 |
| Completed: | 16:05:27 29-01-13 |
| Elapsed: | 00 hrs 10 mins 18 secs |