
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/372947/COADREAD-TP.rppa.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/372947/COADREAD-TP.rppa.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/372947/COADREAD-TP.rppa.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/372947/COADREAD-TP.clin.merged.picked.clindata.txt", "-cP=1", "-cQ=0.05", "-nV=Nozzle.R1", "-OP=RPPA_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] "PRIMARY.SITE.OF.DISEASE"
[1] "GENDER"
[1] "HISTOLOGICAL.TYPE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
[1] "PATHOLOGICSPREAD(M)"
[1] "TUMOR.STAGE"
[1] "RADIATIONS.RADIATION.REGIMENINDICATION"
[1] "COMPLETENESS.OF.RESECTION"
[1] "NUMBER.OF.LYMPH.NODES"
[1] 6
                                       Clinical feature                        
Time to Death                          "Time to Death"                         
AGE                                    "AGE"                                   
PRIMARY.SITE.OF.DISEASE                "PRIMARY SITE OF DISEASE"               
GENDER                                 "GENDER"                                
HISTOLOGICAL.TYPE                      "HISTOLOGICAL TYPE"                     
PATHOLOGY.T                            "PATHOLOGY T"                           
PATHOLOGY.N                            "PATHOLOGY N"                           
PATHOLOGICSPREAD(M)                    "PATHOLOGICSPREAD(M)"                   
TUMOR.STAGE                            "TUMOR STAGE"                           
RADIATIONS.RADIATION.REGIMENINDICATION "RADIATIONS RADIATION REGIMENINDICATION"
COMPLETENESS.OF.RESECTION              "COMPLETENESS OF RESECTION"             
NUMBER.OF.LYMPH.NODES                  "NUMBER OF LYMPH NODES"                 
                                       Statistical test           
Time to Death                          "Cox regression test"      
AGE                                    "Spearman correlation test"
PRIMARY.SITE.OF.DISEASE                "t test"                   
GENDER                                 "t test"                   
HISTOLOGICAL.TYPE                      "ANOVA test"               
PATHOLOGY.T                            "Spearman correlation test"
PATHOLOGY.N                            "Spearman correlation test"
PATHOLOGICSPREAD(M)                    "ANOVA test"               
TUMOR.STAGE                            "Spearman correlation test"
RADIATIONS.RADIATION.REGIMENINDICATION "t test"                   
COMPLETENESS.OF.RESECTION              "ANOVA test"               
NUMBER.OF.LYMPH.NODES                  "Spearman correlation test"
                                       Significant genes
Time to Death                          "N=0"            
AGE                                    "N=0"            
PRIMARY.SITE.OF.DISEASE                "N=72"           
GENDER                                 "N=0"            
HISTOLOGICAL.TYPE                      "N=59"           
PATHOLOGY.T                            "N=1"            
PATHOLOGY.N                            "N=8"            
PATHOLOGICSPREAD(M)                    "N=0"            
TUMOR.STAGE                            "N=7"            
RADIATIONS.RADIATION.REGIMENINDICATION "N=0"            
COMPLETENESS.OF.RESECTION              "N=1"            
NUMBER.OF.LYMPH.NODES                  "N=11"           
                                       Associated with               
Time to Death                          " "                           
AGE                                    " "                           
PRIMARY.SITE.OF.DISEASE                "rectum"                      
GENDER                                 " "                           
HISTOLOGICAL.TYPE                      " "                           
PATHOLOGY.T                            "higher pT"                   
PATHOLOGY.N                            "higher pN"                   
PATHOLOGICSPREAD(M)                    " "                           
TUMOR.STAGE                            "higher stage"                
RADIATIONS.RADIATION.REGIMENINDICATION " "                           
COMPLETENESS.OF.RESECTION              " "                           
NUMBER.OF.LYMPH.NODES                  "higher number.of.lymph.nodes"
                                       &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Time to Death                          " "                                                                                       
AGE                                    " "                                                                                       
PRIMARY.SITE.OF.DISEASE                "N=0"                                                                                     
GENDER                                 " "                                                                                       
HISTOLOGICAL.TYPE                      " "                                                                                       
PATHOLOGY.T                            "N=1"                                                                                     
PATHOLOGY.N                            "N=4"                                                                                     
PATHOLOGICSPREAD(M)                    " "                                                                                       
TUMOR.STAGE                            "N=3"                                                                                     
RADIATIONS.RADIATION.REGIMENINDICATION " "                                                                                       
COMPLETENESS.OF.RESECTION              " "                                                                                       
NUMBER.OF.LYMPH.NODES                  "N=4"                                                                                     
                                       Associated with                     
Time to Death                          " "                           " "   
AGE                                    " "                           " "   
PRIMARY.SITE.OF.DISEASE                "colon"                       "N=72"
GENDER                                 " "                           " "   
HISTOLOGICAL.TYPE                      " "                           " "   
PATHOLOGY.T                            "lower pT"                    "N=0" 
PATHOLOGY.N                            "lower pN"                    "N=4" 
PATHOLOGICSPREAD(M)                    " "                           " "   
TUMOR.STAGE                            "lower stage"                 "N=4" 
RADIATIONS.RADIATION.REGIMENINDICATION " "                           " "   
COMPLETENESS.OF.RESECTION              " "                           " "   
NUMBER.OF.LYMPH.NODES                  "lower number.of.lymph.nodes" "N=7" 
> q(save="no")
