
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/479122/KICH-TP.meth.by_min_expr_corr.data.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/479122/KICH-TP.meth.by_min_expr_corr.data.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/479122/KICH-TP.meth.by_min_expr_corr.data.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/479122/KICH-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] "NEOPLASM.DISEASESTAGE"
[1] "PATHOLOGY.T.STAGE"
[1] "PATHOLOGY.N.STAGE"
[1] "PATHOLOGY.M.STAGE"
[1] "GENDER"
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "NUMBERPACKYEARSSMOKED"
[1] "YEAROFTOBACCOSMOKINGONSET"
[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"                     
KARNOFSKY.PERFORMANCE.SCORE "KARNOFSKY PERFORMANCE SCORE"
NUMBERPACKYEARSSMOKED       "NUMBERPACKYEARSSMOKED"      
YEAROFTOBACCOSMOKINGONSET   "YEAROFTOBACCOSMOKINGONSET"  
                            Statistical test            Significant genes
Time to Death               "Cox regression test"       "N=1"            
AGE                         "Spearman correlation test" "N=0"            
NEOPLASM.DISEASESTAGE       "ANOVA test"                "N=58"           
PATHOLOGY.T.STAGE           "Spearman correlation test" "N=1"            
PATHOLOGY.N.STAGE           "Spearman correlation test" "N=0"            
PATHOLOGY.M.STAGE           "ANOVA test"                "N=53"           
GENDER                      "t test"                    "N=0"            
KARNOFSKY.PERFORMANCE.SCORE "Spearman correlation test" "N=0"            
NUMBERPACKYEARSSMOKED       "Spearman correlation test" "N=1"            
YEAROFTOBACCOSMOKINGONSET   "Spearman correlation test" "N=0"            
                            Associated with               
Time to Death               "shorter survival"            
AGE                         " "                           
NEOPLASM.DISEASESTAGE       " "                           
PATHOLOGY.T.STAGE           "higher stage"                
PATHOLOGY.N.STAGE           " "                           
PATHOLOGY.M.STAGE           " "                           
GENDER                      " "                           
KARNOFSKY.PERFORMANCE.SCORE " "                           
NUMBERPACKYEARSSMOKED       "higher numberpackyearssmoked"
YEAROFTOBACCOSMOKINGONSET   " "                           
                            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Time to Death               "N=0"                                                                                     
AGE                         " "                                                                                       
NEOPLASM.DISEASESTAGE       " "                                                                                       
PATHOLOGY.T.STAGE           "N=1"                                                                                     
PATHOLOGY.N.STAGE           " "                                                                                       
PATHOLOGY.M.STAGE           " "                                                                                       
GENDER                      " "                                                                                       
KARNOFSKY.PERFORMANCE.SCORE " "                                                                                       
NUMBERPACKYEARSSMOKED       "N=1"                                                                                     
YEAROFTOBACCOSMOKINGONSET   " "                                                                                       
                            Associated with                    
Time to Death               "longer survival"             "N=1"
AGE                         " "                           " "  
NEOPLASM.DISEASESTAGE       " "                           " "  
PATHOLOGY.T.STAGE           "lower stage"                 "N=0"
PATHOLOGY.N.STAGE           " "                           " "  
PATHOLOGY.M.STAGE           " "                           " "  
GENDER                      " "                           " "  
KARNOFSKY.PERFORMANCE.SCORE " "                           " "  
NUMBERPACKYEARSSMOKED       "lower numberpackyearssmoked" "N=0"
YEAROFTOBACCOSMOKINGONSET   " "                           " "  
> q(save="no")
