| getCNExpCorrelation1 reducedseg | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/BRCA-TP/8266076/Gistic2_Analysis_8266108/all_data_by_genes.txt |
| getCNExpCorrelation1 mrnaexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/BRCA-TP/8100367/BRCA-TP.medianexp.txt |
| getCNExpCorrelation1 featurename | Hybridization.REF |
| getCNExpCorrelation1 threshold | none |
| getCNExpCorrelation1 method | pearson |
| getCNExpCorrelation1 cortablename | BRCA-TP |
| getCNExpCorrelation1 figurename | OUTPUT |
| getCNExpCorrelation1 qatablename | STATS |
| writeCorReport2 type | mRNA |
| Execution Times: | |
| Submitted: | 10:48:22 03-05-14 |
| Completed: | |
| Elapsed: | 00 hrs 02 mins 50 secs |
step 1. getCNExpCorrelation [id: 513333] Calculates the correlations between the copy number and expression data
urn:lsid:broadinstitute.org:cancer.genome.analysis:00287:19
| reducedseg | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/BRCA-TP/8266076/Gistic2_Analysis_8266108/all_data_by_genes.txt |
| mrnaexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/BRCA-TP/8100367/BRCA-TP.medianexp.txt |
| featurename | Hybridization.REF |
| threshold | none |
| method | pearson |
| cortablename | BRCA-TP |
| figurename | OUTPUT |
| qatablename | STATS |
| Output Files: | |
| BRCA-TP.CORS.tsv | |
| STATS.QA.tsv | |
| .lsf.out | |
| OUTPUT.CORS.png | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 10:48:22 03-05-14 |
| Completed: | 10:50:57 03-05-14 |
| Elapsed: | 00 hrs 02 mins 34 secs |
step 2. writeCorReport [id: 513334] Generates the html report based on the correlation data
urn:lsid:broadinstitute.org:cancer.genome.analysis:00288:42
| pngname | OUTPUT.CORS.png |
| tablename | BRCA-TP.CORS.tsv |
| type | mRNA |
| qatablename | STATS.QA.tsv |
| Output Files: | |
| nozzle.html | |
| nozzle.RData | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 10:48:22 03-05-14 |
| Completed: | 10:51:12 03-05-14 |
| Elapsed: | 00 hrs 02 mins 49 secs |
