
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/175341/PRAD.uncv2.mRNAseq_RSEM_normalized_log2.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/175341/PRAD.uncv2.mRNAseq_RSEM_normalized_log2.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/175341/PRAD.uncv2.mRNAseq_RSEM_normalized_log2.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/175341/PRAD.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] "AGE"
[1] "RADIATIONS.RADIATION.REGIMENINDICATION"
[1] "NEOADJUVANT.THERAPY"
[1] 6
                                       Clinical feature                        
AGE                                    "AGE"                                   
RADIATIONS.RADIATION.REGIMENINDICATION "RADIATIONS RADIATION REGIMENINDICATION"
NEOADJUVANT.THERAPY                    "NEOADJUVANT THERAPY"                   
                                       Statistical test           
AGE                                    "Spearman correlation test"
RADIATIONS.RADIATION.REGIMENINDICATION "t test"                   
NEOADJUVANT.THERAPY                    "t test"                   
                                       Significant genes Associated with
AGE                                    "N=1"             "older"        
RADIATIONS.RADIATION.REGIMENINDICATION "N=10"            "yes"          
NEOADJUVANT.THERAPY                    "N=77"            "yes"          
                                       &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
AGE                                    "N=0"                                                                                     
RADIATIONS.RADIATION.REGIMENINDICATION "N=3"                                                                                     
NEOADJUVANT.THERAPY                    "N=59"                                                                                    
                                       Associated with       
AGE                                    "younger"       "N=1" 
RADIATIONS.RADIATION.REGIMENINDICATION "no"            "N=7" 
NEOADJUVANT.THERAPY                    "no"            "N=18"
> q(save="no")
