
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/475785/PRAD-TP.meth.by_min_expr_corr.data.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/475785/PRAD-TP.meth.by_min_expr_corr.data.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/475785/PRAD-TP.meth.by_min_expr_corr.data.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/475785/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] "PATHOLOGY.T.STAGE"
[1] "PATHOLOGY.N.STAGE"
[1] "COMPLETENESS.OF.RESECTION"
[1] "NUMBER.OF.LYMPH.NODES"
[1] 6
                          Clinical feature           
AGE                       "AGE"                      
PATHOLOGY.T.STAGE         "PATHOLOGY T STAGE"        
PATHOLOGY.N.STAGE         "PATHOLOGY N STAGE"        
COMPLETENESS.OF.RESECTION "COMPLETENESS OF RESECTION"
NUMBER.OF.LYMPH.NODES     "NUMBER OF LYMPH NODES"    
                          Statistical test            Significant genes
AGE                       "Spearman correlation test" "N=1"            
PATHOLOGY.T.STAGE         "Spearman correlation test" "N=0"            
PATHOLOGY.N.STAGE         "t test"                    "N=15"           
COMPLETENESS.OF.RESECTION "ANOVA test"                "N=7"            
NUMBER.OF.LYMPH.NODES     "Spearman correlation test" "N=0"            
                          Associated with
AGE                       "older"        
PATHOLOGY.T.STAGE         " "            
PATHOLOGY.N.STAGE         "class1"       
COMPLETENESS.OF.RESECTION " "            
NUMBER.OF.LYMPH.NODES     " "            
                          &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
AGE                       "N=1"                                                                                     
PATHOLOGY.T.STAGE         " "                                                                                       
PATHOLOGY.N.STAGE         "N=0"                                                                                     
COMPLETENESS.OF.RESECTION " "                                                                                       
NUMBER.OF.LYMPH.NODES     " "                                                                                       
                          Associated with       
AGE                       "younger"       "N=0" 
PATHOLOGY.T.STAGE         " "             " "   
PATHOLOGY.N.STAGE         "class0"        "N=15"
COMPLETENESS.OF.RESECTION " "             " "   
NUMBER.OF.LYMPH.NODES     " "             " "   
> q(save="no")
