
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/286645/READ-TP.medianexp.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286645/READ-TP.medianexp.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286645/READ-TP.medianexp.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286645/READ-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] "GENDER"
[1] "HISTOLOGICAL.TYPE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
[1] "PATHOLOGICSPREAD(M)"
[1] "TUMOR.STAGE"
[1] 6
                    Clinical feature      Statistical test           
Time to Death       "Time to Death"       "Cox regression test"      
AGE                 "AGE"                 "Spearman correlation test"
GENDER              "GENDER"              "t test"                   
HISTOLOGICAL.TYPE   "HISTOLOGICAL TYPE"   "t test"                   
PATHOLOGY.T         "PATHOLOGY T"         "Spearman correlation test"
PATHOLOGY.N         "PATHOLOGY N"         "Spearman correlation test"
PATHOLOGICSPREAD(M) "PATHOLOGICSPREAD(M)" "t test"                   
TUMOR.STAGE         "TUMOR STAGE"         "Spearman correlation test"
                    Significant genes Associated with                 
Time to Death       "N=0"             " "                             
AGE                 "N=0"             " "                             
GENDER              "N=11"            "male"                          
HISTOLOGICAL.TYPE   "N=12"            "rectal mucinous adenocarcinoma"
PATHOLOGY.T         "N=0"             " "                             
PATHOLOGY.N         "N=0"             " "                             
PATHOLOGICSPREAD(M) "N=0"             " "                             
TUMOR.STAGE         "N=0"             " "                             
                    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Time to Death       " "                                                                                       
AGE                 " "                                                                                       
GENDER              "N=11"                                                                                    
HISTOLOGICAL.TYPE   "N=6"                                                                                     
PATHOLOGY.T         " "                                                                                       
PATHOLOGY.N         " "                                                                                       
PATHOLOGICSPREAD(M) " "                                                                                       
TUMOR.STAGE         " "                                                                                       
                    Associated with              
Time to Death       " "                     " "  
AGE                 " "                     " "  
GENDER              "female"                "N=0"
HISTOLOGICAL.TYPE   "rectal adenocarcinoma" "N=6"
PATHOLOGY.T         " "                     " "  
PATHOLOGY.N         " "                     " "  
PATHOLOGICSPREAD(M) " "                     " "  
TUMOR.STAGE         " "                     " "  
> q(save="no")
