
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/479152/KIRC-TP.medianexp.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/479152/KIRC-TP.medianexp.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/479152/KIRC-TP.medianexp.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/479152/KIRC-TP.clin.merged.picked.clindata.txt", "-cP=1", "-cQ=0.05", "-nV=Nozzle.R1", "-OP=MRNA_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] "NEOPLASM.DISEASESTAGE"
[1] "PATHOLOGY.T.STAGE"
[1] "PATHOLOGY.N.STAGE"
[1] "PATHOLOGY.M.STAGE"
[1] "GENDER"
[1] 6
                      Clinical feature        Statistical test           
Time to Death         "Time to Death"         "Cox regression test"      
AGE                   "AGE"                   "Spearman correlation test"
NEOPLASM.DISEASESTAGE "NEOPLASM DISEASESTAGE" "ANOVA test"               
PATHOLOGY.T.STAGE     "PATHOLOGY T STAGE"     "Spearman correlation test"
PATHOLOGY.N.STAGE     "PATHOLOGY N STAGE"     "t test"                   
PATHOLOGY.M.STAGE     "PATHOLOGY M STAGE"     "t test"                   
GENDER                "GENDER"                "t test"                   
                      Significant genes Associated with
Time to Death         "N=0"             " "            
AGE                   "N=0"             " "            
NEOPLASM.DISEASESTAGE "N=66"            " "            
PATHOLOGY.T.STAGE     "N=0"             " "            
PATHOLOGY.N.STAGE     "N=94"            "class1"       
PATHOLOGY.M.STAGE     "N=64"            "m1"           
GENDER                "N=13"            "male"         
                      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Time to Death         " "                                                                                       
AGE                   " "                                                                                       
NEOPLASM.DISEASESTAGE " "                                                                                       
PATHOLOGY.T.STAGE     " "                                                                                       
PATHOLOGY.N.STAGE     "N=52"                                                                                    
PATHOLOGY.M.STAGE     "N=23"                                                                                    
GENDER                "N=13"                                                                                    
                      Associated with       
Time to Death         " "             " "   
AGE                   " "             " "   
NEOPLASM.DISEASESTAGE " "             " "   
PATHOLOGY.T.STAGE     " "             " "   
PATHOLOGY.N.STAGE     "class0"        "N=42"
PATHOLOGY.M.STAGE     "m0"            "N=41"
GENDER                "female"        "N=0" 
> q(save="no")
