
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ClinicalAnalysisAllGenesReport_nozzle.29.3859/ClinicalAnalysisAllGenesReport_nozzle.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ClinicalAnalysisAllGenesReport_nozzle.29.3859/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iR=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/395739/OV-TP.uncv2.mRNAseq_RSEM_normalized_log2.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/395739/OV-TP.uncv2.mRNAseq_RSEM_normalized_log2.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/395739/OV-TP.uncv2.mRNAseq_RSEM_normalized_log2.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/395739/OV-TP.clin.merged.picked.clindata.txt", "-cP=1", "-cQ=0.05", "-nV=Nozzle.R1", "-OP=MRNASEQ_EXPR", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "dx"   "-iX="
[1] "dx" " " 
[1] "dx" " " 
[1] "Time to Death"
[1] "AGE"
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "TUMOR.STAGE"
[1] 6
                            Clinical feature             
Time to Death               "Time to Death"              
AGE                         "AGE"                        
KARNOFSKY.PERFORMANCE.SCORE "KARNOFSKY PERFORMANCE SCORE"
TUMOR.STAGE                 "TUMOR STAGE"                
                            Statistical test            Significant genes
Time to Death               "Cox regression test"       "N=1"            
AGE                         "Spearman correlation test" "N=57"           
KARNOFSKY.PERFORMANCE.SCORE "Spearman correlation test" "N=0"            
TUMOR.STAGE                 "Spearman correlation test" "N=1"            
                            Associated with   
Time to Death               "shorter survival"
AGE                         "older"           
KARNOFSKY.PERFORMANCE.SCORE " "               
TUMOR.STAGE                 "higher stage"    
                            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Time to Death               "N=0"                                                                                     
AGE                         "N=30"                                                                                    
KARNOFSKY.PERFORMANCE.SCORE " "                                                                                       
TUMOR.STAGE                 "N=1"                                                                                     
                            Associated with         
Time to Death               "longer survival" "N=1" 
AGE                         "younger"         "N=27"
KARNOFSKY.PERFORMANCE.SCORE " "               " "   
TUMOR.STAGE                 "lower stage"     "N=0" 
> q(save="no")
