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

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> 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/226427/BLCA.miRseq_RPKM_log2.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/226427/BLCA.miRseq_RPKM_log2.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/226427/BLCA.miRseq_RPKM_log2.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/226427/BLCA.clin.merged.picked.clindata.txt", "-cP=1", "-cQ=0.05", "-nV=Nozzle.R1", "-OP=MIRNASEQ_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] "GENDER"
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] 6
                            Clinical feature             
Time to Death               "Time to Death"              
AGE                         "AGE"                        
GENDER                      "GENDER"                     
KARNOFSKY.PERFORMANCE.SCORE "KARNOFSKY PERFORMANCE SCORE"
                            Statistical test            Significant genes
Time to Death               "Cox regression test"       "N=0"            
AGE                         "Spearman correlation test" "N=0"            
GENDER                      "t test"                    "N=0"            
KARNOFSKY.PERFORMANCE.SCORE "Spearman correlation test" "N=0"            
                            Associated with
Time to Death               " "            
AGE                         " "            
GENDER                      " "            
KARNOFSKY.PERFORMANCE.SCORE " "            
                            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Time to Death               " "                                                                                       
AGE                         " "                                                                                       
GENDER                      " "                                                                                       
KARNOFSKY.PERFORMANCE.SCORE " "                                                                                       
                            Associated with    
Time to Death               " "             " "
AGE                         " "             " "
GENDER                      " "             " "
KARNOFSKY.PERFORMANCE.SCORE " "             " "
> q(save="no")
