
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/302782/PRAD-TP.meth.for_correlation.filtered_data.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/302782/PRAD-TP.meth.for_correlation.filtered_data.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/302782/PRAD-TP.meth.for_correlation.filtered_data.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/302782/PRAD-TP.clin.merged.picked.clindata.txt", "-cP=1", "-cQ=0.05", "-nV=Nozzle.R1", "-OP=METHYLATION", "-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] 6
                                       Clinical feature                        
AGE                                    "AGE"                                   
RADIATIONS.RADIATION.REGIMENINDICATION "RADIATIONS RADIATION REGIMENINDICATION"
                                       Statistical test           
AGE                                    "Spearman correlation test"
RADIATIONS.RADIATION.REGIMENINDICATION "t test"                   
                                       Significant genes Associated with
AGE                                    "N=2"             "older"        
RADIATIONS.RADIATION.REGIMENINDICATION "N=54"            "yes"          
                                       &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
AGE                                    "N=2"                                                                                     
RADIATIONS.RADIATION.REGIMENINDICATION "N=42"                                                                                    
                                       Associated with       
AGE                                    "younger"       "N=0" 
RADIATIONS.RADIATION.REGIMENINDICATION "no"            "N=12"
> q(save="no")
