
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/332521/BLCA-TP.meth.for_correlation.filtered_data.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/332521/BLCA-TP.meth.for_correlation.filtered_data.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/332521/BLCA-TP.meth.for_correlation.filtered_data.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/332521/BLCA-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] "NUMBERPACKYEARSSMOKED"
[1] "STOPPEDSMOKINGYEAR"
[1] "TOBACCOSMOKINGHISTORYINDICATOR"
[1] "DISTANT.METASTASIS"
[1] "LYMPH.NODE.METASTASIS"
[1] "NUMBER.OF.LYMPH.NODES"
[1] "NEOPLASM.DISEASESTAGE"
[1] 6
                               Clinical feature                
Time to Death                  "Time to Death"                 
AGE                            "AGE"                           
GENDER                         "GENDER"                        
KARNOFSKY.PERFORMANCE.SCORE    "KARNOFSKY PERFORMANCE SCORE"   
NUMBERPACKYEARSSMOKED          "NUMBERPACKYEARSSMOKED"         
STOPPEDSMOKINGYEAR             "STOPPEDSMOKINGYEAR"            
TOBACCOSMOKINGHISTORYINDICATOR "TOBACCOSMOKINGHISTORYINDICATOR"
DISTANT.METASTASIS             "DISTANT METASTASIS"            
LYMPH.NODE.METASTASIS          "LYMPH NODE METASTASIS"         
NUMBER.OF.LYMPH.NODES          "NUMBER OF LYMPH NODES"         
NEOPLASM.DISEASESTAGE          "NEOPLASM DISEASESTAGE"         
                               Statistical test            Significant genes
Time to Death                  "Cox regression test"       "N=0"            
AGE                            "Spearman correlation test" "N=0"            
GENDER                         "t test"                    "N=15"           
KARNOFSKY.PERFORMANCE.SCORE    "Spearman correlation test" "N=0"            
NUMBERPACKYEARSSMOKED          "Spearman correlation test" "N=0"            
STOPPEDSMOKINGYEAR             "Spearman correlation test" "N=0"            
TOBACCOSMOKINGHISTORYINDICATOR "Spearman correlation test" "N=0"            
DISTANT.METASTASIS             "ANOVA test"                "N=2"            
LYMPH.NODE.METASTASIS          "ANOVA test"                "N=4"            
NUMBER.OF.LYMPH.NODES          "Spearman correlation test" "N=1"            
NEOPLASM.DISEASESTAGE          "ANOVA test"                "N=0"            
                               Associated with               
Time to Death                  " "                           
AGE                            " "                           
GENDER                         "male"                        
KARNOFSKY.PERFORMANCE.SCORE    " "                           
NUMBERPACKYEARSSMOKED          " "                           
STOPPEDSMOKINGYEAR             " "                           
TOBACCOSMOKINGHISTORYINDICATOR " "                           
DISTANT.METASTASIS             " "                           
LYMPH.NODE.METASTASIS          " "                           
NUMBER.OF.LYMPH.NODES          "higher number.of.lymph.nodes"
NEOPLASM.DISEASESTAGE          " "                           
                               &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Time to Death                  " "                                                                                       
AGE                            " "                                                                                       
GENDER                         "N=2"                                                                                     
KARNOFSKY.PERFORMANCE.SCORE    " "                                                                                       
NUMBERPACKYEARSSMOKED          " "                                                                                       
STOPPEDSMOKINGYEAR             " "                                                                                       
TOBACCOSMOKINGHISTORYINDICATOR " "                                                                                       
DISTANT.METASTASIS             " "                                                                                       
LYMPH.NODE.METASTASIS          " "                                                                                       
NUMBER.OF.LYMPH.NODES          "N=0"                                                                                     
NEOPLASM.DISEASESTAGE          " "                                                                                       
                               Associated with                     
Time to Death                  " "                           " "   
AGE                            " "                           " "   
GENDER                         "female"                      "N=13"
KARNOFSKY.PERFORMANCE.SCORE    " "                           " "   
NUMBERPACKYEARSSMOKED          " "                           " "   
STOPPEDSMOKINGYEAR             " "                           " "   
TOBACCOSMOKINGHISTORYINDICATOR " "                           " "   
DISTANT.METASTASIS             " "                           " "   
LYMPH.NODE.METASTASIS          " "                           " "   
NUMBER.OF.LYMPH.NODES          "lower number.of.lymph.nodes" "N=1" 
NEOPLASM.DISEASESTAGE          " "                           " "   
> q(save="no")
