
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/473073/COAD-TP.medianexp.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/473073/COAD-TP.medianexp.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/473073/COAD-TP.medianexp.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/473073/COAD-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] "NEOPLASM.DISEASESTAGE"
[1] "PATHOLOGY.T.STAGE"
[1] "PATHOLOGY.N.STAGE"
[1] "PATHOLOGY.M.STAGE"
[1] "GENDER"
[1] "HISTOLOGICAL.TYPE"
[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"        
COMPLETENESS.OF.RESECTION "COMPLETENESS OF RESECTION"
NUMBER.OF.LYMPH.NODES     "NUMBER OF LYMPH NODES"    
                          Statistical test            Significant genes
Time to Death             "Cox regression test"       "N=0"            
AGE                       "Spearman correlation test" "N=1"            
NEOPLASM.DISEASESTAGE     "ANOVA test"                "N=2"            
PATHOLOGY.T.STAGE         "Spearman correlation test" "N=0"            
PATHOLOGY.N.STAGE         "Spearman correlation test" "N=0"            
PATHOLOGY.M.STAGE         "ANOVA test"                "N=1"            
GENDER                    "t test"                    "N=19"           
HISTOLOGICAL.TYPE         "t test"                    "N=80"           
COMPLETENESS.OF.RESECTION "ANOVA test"                "N=49"           
NUMBER.OF.LYMPH.NODES     "Spearman correlation test" "N=0"            
                          Associated with                
Time to Death             " "                            
AGE                       "older"                        
NEOPLASM.DISEASESTAGE     " "                            
PATHOLOGY.T.STAGE         " "                            
PATHOLOGY.N.STAGE         " "                            
PATHOLOGY.M.STAGE         " "                            
GENDER                    "male"                         
HISTOLOGICAL.TYPE         "colon mucinous adenocarcinoma"
COMPLETENESS.OF.RESECTION " "                            
NUMBER.OF.LYMPH.NODES     " "                            
                          &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Time to Death             " "                                                                                       
AGE                       "N=0"                                                                                     
NEOPLASM.DISEASESTAGE     " "                                                                                       
PATHOLOGY.T.STAGE         " "                                                                                       
PATHOLOGY.N.STAGE         " "                                                                                       
PATHOLOGY.M.STAGE         " "                                                                                       
GENDER                    "N=13"                                                                                    
HISTOLOGICAL.TYPE         "N=40"                                                                                    
COMPLETENESS.OF.RESECTION " "                                                                                       
NUMBER.OF.LYMPH.NODES     " "                                                                                       
                          Associated with              
Time to Death             " "                    " "   
AGE                       "younger"              "N=1" 
NEOPLASM.DISEASESTAGE     " "                    " "   
PATHOLOGY.T.STAGE         " "                    " "   
PATHOLOGY.N.STAGE         " "                    " "   
PATHOLOGY.M.STAGE         " "                    " "   
GENDER                    "female"               "N=6" 
HISTOLOGICAL.TYPE         "colon adenocarcinoma" "N=40"
COMPLETENESS.OF.RESECTION " "                    " "   
NUMBER.OF.LYMPH.NODES     " "                    " "   
> q(save="no")
