
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/373474/PRAD-TP.meth.for_correlation.filtered_data.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/373474/PRAD-TP.meth.for_correlation.filtered_data.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/373474/PRAD-TP.meth.for_correlation.filtered_data.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/373474/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] "COMPLETENESS.OF.RESECTION"
[1] "NUMBER.OF.LYMPH.NODES"
[1] 6
                                       Clinical feature                        
AGE                                    "AGE"                                   
RADIATIONS.RADIATION.REGIMENINDICATION "RADIATIONS RADIATION REGIMENINDICATION"
COMPLETENESS.OF.RESECTION              "COMPLETENESS OF RESECTION"             
NUMBER.OF.LYMPH.NODES                  "NUMBER OF LYMPH NODES"                 
                                       Statistical test           
AGE                                    "Spearman correlation test"
RADIATIONS.RADIATION.REGIMENINDICATION "t test"                   
COMPLETENESS.OF.RESECTION              "ANOVA test"               
NUMBER.OF.LYMPH.NODES                  "Spearman correlation test"
                                       Significant genes Associated with
AGE                                    "N=0"             " "            
RADIATIONS.RADIATION.REGIMENINDICATION "N=89"            "yes"          
COMPLETENESS.OF.RESECTION              "N=4"             " "            
NUMBER.OF.LYMPH.NODES                  "N=0"             " "            
                                       &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
AGE                                    " "                                                                                       
RADIATIONS.RADIATION.REGIMENINDICATION "N=56"                                                                                    
COMPLETENESS.OF.RESECTION              " "                                                                                       
NUMBER.OF.LYMPH.NODES                  " "                                                                                       
                                       Associated with       
AGE                                    " "             " "   
RADIATIONS.RADIATION.REGIMENINDICATION "no"            "N=33"
COMPLETENESS.OF.RESECTION              " "             " "   
NUMBER.OF.LYMPH.NODES                  " "             " "   
> q(save="no")
