| ClinicalAnalysisAllGenes_new1 data file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/LUAD/1768802/0.GDAC_mRNA_Preprocess_Median.Finished/LUAD.medianexp.txt |
| ClinicalAnalysisAllGenes_new1 clinical file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LUAD/1709124/1.GDAC_clinicalDataPicker.Finished/LUAD.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: | 05:20:53 04-10-12 |
| Completed: | |
| Elapsed: | 00 hrs 10 mins 17 secs |
step 1. ClinicalAnalysisAllGenes_new [id: 175943] 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/LUAD/1768802/0.GDAC_mRNA_Preprocess_Median.Finished/LUAD.medianexp.txt |
| clinical file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LUAD/1709124/1.GDAC_clinicalDataPicker.Finished/LUAD.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: | |
| LUAD.medianexp.exprdata.gct | |
| LUAD.clin.merged.picked.clindata.txt | |
| LUAD.medianexp.clinical.results.txt | |
| LUAD.medianexp.analysis.results.RData | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 05:21:33 04-10-12 |
| Completed: | 05:27:45 04-10-12 |
| Elapsed: | 00 hrs 06 mins 12 secs |
step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 175944] Generate a report to summarize the results from ClinicalAnalysisAllGenes module
urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:29
| all result file | LUAD.medianexp.clinical.results.txt |
| RData file | LUAD.medianexp.analysis.results.RData |
| expression file | LUAD.medianexp.exprdata.gct |
| clinical file | LUAD.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 |
| Output Files: | |
| table1.txt | |
| supp.table1.txt | |
| table8.txt | |
| table5.txt | |
| V3ex.png | |
| V5ex.png | |
| nozzle.RData | |
| V5ex.pdf | |
| V3ex.pdf | |
| nozzle.html | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 05:21:33 04-10-12 |
| Completed: | 05:31:10 04-10-12 |
| Elapsed: | 00 hrs 09 mins 36 secs |