
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/421053/KIRP-TP.meth.by_min_expr_corr.data.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/421053/KIRP-TP.meth.by_min_expr_corr.data.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/421053/KIRP-TP.meth.by_min_expr_corr.data.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/421053/KIRP-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] "Time to Death"
[1] "AGE"
[1] "GENDER"
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "DISTANT.METASTASIS"
[1] "LYMPH.NODE.METASTASIS"
[1] "NEOPLASM.DISEASESTAGE"
[1] 6
                            Clinical feature             
Time to Death               "Time to Death"              
AGE                         "AGE"                        
GENDER                      "GENDER"                     
KARNOFSKY.PERFORMANCE.SCORE "KARNOFSKY PERFORMANCE SCORE"
DISTANT.METASTASIS          "DISTANT METASTASIS"         
LYMPH.NODE.METASTASIS       "LYMPH NODE METASTASIS"      
NEOPLASM.DISEASESTAGE       "NEOPLASM DISEASESTAGE"      
                            Statistical test            Significant genes
Time to Death               "Cox regression test"       "N=41"           
AGE                         "Spearman correlation test" "N=2"            
GENDER                      "t test"                    "N=5"            
KARNOFSKY.PERFORMANCE.SCORE "Spearman correlation test" "N=0"            
DISTANT.METASTASIS          "ANOVA test"                "N=104"          
LYMPH.NODE.METASTASIS       "ANOVA test"                "N=234"          
NEOPLASM.DISEASESTAGE       "ANOVA test"                "N=119"          
                            Associated with   
Time to Death               "shorter survival"
AGE                         "older"           
GENDER                      "male"            
KARNOFSKY.PERFORMANCE.SCORE " "               
DISTANT.METASTASIS          " "               
LYMPH.NODE.METASTASIS       " "               
NEOPLASM.DISEASESTAGE       " "               
                            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Time to Death               "N=40"                                                                                    
AGE                         "N=0"                                                                                     
GENDER                      "N=3"                                                                                     
KARNOFSKY.PERFORMANCE.SCORE " "                                                                                       
DISTANT.METASTASIS          " "                                                                                       
LYMPH.NODE.METASTASIS       " "                                                                                       
NEOPLASM.DISEASESTAGE       " "                                                                                       
                            Associated with        
Time to Death               "longer survival" "N=1"
AGE                         "younger"         "N=2"
GENDER                      "female"          "N=2"
KARNOFSKY.PERFORMANCE.SCORE " "               " "  
DISTANT.METASTASIS          " "               " "  
LYMPH.NODE.METASTASIS       " "               " "  
NEOPLASM.DISEASESTAGE       " "               " "  
> q(save="no")
