
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/473040/COAD-TP.rppa.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/473040/COAD-TP.rppa.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/473040/COAD-TP.rppa.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/473040/COAD-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] "NEOPLASM.DISEASESTAGE"
[1] "PATHOLOGY.T.STAGE"
[1] "PATHOLOGY.N.STAGE"
[1] "PATHOLOGY.M.STAGE"
[1] "GENDER"
[1] "HISTOLOGICAL.TYPE"
[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"                                   
NEOPLASM.DISEASESTAGE                  "NEOPLASM DISEASESTAGE"                 
PATHOLOGY.T.STAGE                      "PATHOLOGY T STAGE"                     
PATHOLOGY.N.STAGE                      "PATHOLOGY N STAGE"                     
PATHOLOGY.M.STAGE                      "PATHOLOGY M STAGE"                     
GENDER                                 "GENDER"                                
HISTOLOGICAL.TYPE                      "HISTOLOGICAL TYPE"                     
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"
NEOPLASM.DISEASESTAGE                  "ANOVA test"               
PATHOLOGY.T.STAGE                      "Spearman correlation test"
PATHOLOGY.N.STAGE                      "Spearman correlation test"
PATHOLOGY.M.STAGE                      "ANOVA test"               
GENDER                                 "t test"                   
HISTOLOGICAL.TYPE                      "t 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"            
NEOPLASM.DISEASESTAGE                  "N=1"            
PATHOLOGY.T.STAGE                      "N=1"            
PATHOLOGY.N.STAGE                      "N=1"            
PATHOLOGY.M.STAGE                      "N=1"            
GENDER                                 "N=0"            
HISTOLOGICAL.TYPE                      "N=4"            
RADIATIONS.RADIATION.REGIMENINDICATION "N=3"            
COMPLETENESS.OF.RESECTION              "N=2"            
NUMBER.OF.LYMPH.NODES                  "N=1"            
                                       Associated with                
Time to Death                          " "                            
AGE                                    " "                            
NEOPLASM.DISEASESTAGE                  " "                            
PATHOLOGY.T.STAGE                      "higher stage"                 
PATHOLOGY.N.STAGE                      "higher stage"                 
PATHOLOGY.M.STAGE                      " "                            
GENDER                                 " "                            
HISTOLOGICAL.TYPE                      "colon mucinous adenocarcinoma"
RADIATIONS.RADIATION.REGIMENINDICATION "yes"                          
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                                    " "                                                                                       
NEOPLASM.DISEASESTAGE                  " "                                                                                       
PATHOLOGY.T.STAGE                      "N=1"                                                                                     
PATHOLOGY.N.STAGE                      "N=1"                                                                                     
PATHOLOGY.M.STAGE                      " "                                                                                       
GENDER                                 " "                                                                                       
HISTOLOGICAL.TYPE                      "N=2"                                                                                     
RADIATIONS.RADIATION.REGIMENINDICATION "N=2"                                                                                     
COMPLETENESS.OF.RESECTION              " "                                                                                       
NUMBER.OF.LYMPH.NODES                  "N=1"                                                                                     
                                       Associated with                    
Time to Death                          " "                           " "  
AGE                                    " "                           " "  
NEOPLASM.DISEASESTAGE                  " "                           " "  
PATHOLOGY.T.STAGE                      "lower stage"                 "N=0"
PATHOLOGY.N.STAGE                      "lower stage"                 "N=0"
PATHOLOGY.M.STAGE                      " "                           " "  
GENDER                                 " "                           " "  
HISTOLOGICAL.TYPE                      "colon adenocarcinoma"        "N=2"
RADIATIONS.RADIATION.REGIMENINDICATION "no"                          "N=1"
COMPLETENESS.OF.RESECTION              " "                           " "  
NUMBER.OF.LYMPH.NODES                  "lower number.of.lymph.nodes" "N=0"
> q(save="no")
