
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/333749/LUSC-TP.rppa.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/333749/LUSC-TP.rppa.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/333749/LUSC-TP.rppa.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/333749/LUSC-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] "GENDER"
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "HISTOLOGICAL.TYPE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
[1] "PATHOLOGICSPREAD(M)"
[1] "TUMOR.STAGE"
[1] "RADIATIONS.RADIATION.REGIMENINDICATION"
[1] "NUMBERPACKYEARSSMOKED"
[1] "STOPPEDSMOKINGYEAR"
[1] "TOBACCOSMOKINGHISTORYINDICATOR"
[1] "YEAROFTOBACCOSMOKINGONSET"
[1] 6
                                       Clinical feature                        
Time to Death                          "Time to Death"                         
AGE                                    "AGE"                                   
GENDER                                 "GENDER"                                
KARNOFSKY.PERFORMANCE.SCORE            "KARNOFSKY PERFORMANCE SCORE"           
HISTOLOGICAL.TYPE                      "HISTOLOGICAL TYPE"                     
PATHOLOGY.T                            "PATHOLOGY T"                           
PATHOLOGY.N                            "PATHOLOGY N"                           
PATHOLOGICSPREAD(M)                    "PATHOLOGICSPREAD(M)"                   
TUMOR.STAGE                            "TUMOR STAGE"                           
RADIATIONS.RADIATION.REGIMENINDICATION "RADIATIONS RADIATION REGIMENINDICATION"
NUMBERPACKYEARSSMOKED                  "NUMBERPACKYEARSSMOKED"                 
STOPPEDSMOKINGYEAR                     "STOPPEDSMOKINGYEAR"                    
TOBACCOSMOKINGHISTORYINDICATOR         "TOBACCOSMOKINGHISTORYINDICATOR"        
YEAROFTOBACCOSMOKINGONSET              "YEAROFTOBACCOSMOKINGONSET"             
                                       Statistical test           
Time to Death                          "Cox regression test"      
AGE                                    "Spearman correlation test"
GENDER                                 "t test"                   
KARNOFSKY.PERFORMANCE.SCORE            "Spearman correlation test"
HISTOLOGICAL.TYPE                      "ANOVA test"               
PATHOLOGY.T                            "Spearman correlation test"
PATHOLOGY.N                            "Spearman correlation test"
PATHOLOGICSPREAD(M)                    "t test"                   
TUMOR.STAGE                            "Spearman correlation test"
RADIATIONS.RADIATION.REGIMENINDICATION "t test"                   
NUMBERPACKYEARSSMOKED                  "Spearman correlation test"
STOPPEDSMOKINGYEAR                     "Spearman correlation test"
TOBACCOSMOKINGHISTORYINDICATOR         "ANOVA test"               
YEAROFTOBACCOSMOKINGONSET              "Spearman correlation test"
                                       Significant genes
Time to Death                          "N=1"            
AGE                                    "N=2"            
GENDER                                 "N=0"            
KARNOFSKY.PERFORMANCE.SCORE            "N=0"            
HISTOLOGICAL.TYPE                      "N=5"            
PATHOLOGY.T                            "N=2"            
PATHOLOGY.N                            "N=2"            
PATHOLOGICSPREAD(M)                    "N=0"            
TUMOR.STAGE                            "N=3"            
RADIATIONS.RADIATION.REGIMENINDICATION "N=0"            
NUMBERPACKYEARSSMOKED                  "N=0"            
STOPPEDSMOKINGYEAR                     "N=0"            
TOBACCOSMOKINGHISTORYINDICATOR         "N=0"            
YEAROFTOBACCOSMOKINGONSET              "N=1"            
                                       Associated with                   
Time to Death                          "shorter survival"                
AGE                                    "older"                           
GENDER                                 " "                               
KARNOFSKY.PERFORMANCE.SCORE            " "                               
HISTOLOGICAL.TYPE                      " "                               
PATHOLOGY.T                            "higher pT"                       
PATHOLOGY.N                            "higher pN"                       
PATHOLOGICSPREAD(M)                    " "                               
TUMOR.STAGE                            "higher stage"                    
RADIATIONS.RADIATION.REGIMENINDICATION " "                               
NUMBERPACKYEARSSMOKED                  " "                               
STOPPEDSMOKINGYEAR                     " "                               
TOBACCOSMOKINGHISTORYINDICATOR         " "                               
YEAROFTOBACCOSMOKINGONSET              "higher yearoftobaccosmokingonset"
                                       &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Time to Death                          "N=0"                                                                                     
AGE                                    "N=0"                                                                                     
GENDER                                 " "                                                                                       
KARNOFSKY.PERFORMANCE.SCORE            " "                                                                                       
HISTOLOGICAL.TYPE                      " "                                                                                       
PATHOLOGY.T                            "N=2"                                                                                     
PATHOLOGY.N                            "N=0"                                                                                     
PATHOLOGICSPREAD(M)                    " "                                                                                       
TUMOR.STAGE                            "N=1"                                                                                     
RADIATIONS.RADIATION.REGIMENINDICATION " "                                                                                       
NUMBERPACKYEARSSMOKED                  " "                                                                                       
STOPPEDSMOKINGYEAR                     " "                                                                                       
TOBACCOSMOKINGHISTORYINDICATOR         " "                                                                                       
YEAROFTOBACCOSMOKINGONSET              "N=1"                                                                                     
                                       Associated with                        
Time to Death                          "longer survival"                 "N=1"
AGE                                    "younger"                         "N=2"
GENDER                                 " "                               " "  
KARNOFSKY.PERFORMANCE.SCORE            " "                               " "  
HISTOLOGICAL.TYPE                      " "                               " "  
PATHOLOGY.T                            "lower pT"                        "N=0"
PATHOLOGY.N                            "lower pN"                        "N=2"
PATHOLOGICSPREAD(M)                    " "                               " "  
TUMOR.STAGE                            "lower stage"                     "N=2"
RADIATIONS.RADIATION.REGIMENINDICATION " "                               " "  
NUMBERPACKYEARSSMOKED                  " "                               " "  
STOPPEDSMOKINGYEAR                     " "                               " "  
TOBACCOSMOKINGHISTORYINDICATOR         " "                               " "  
YEAROFTOBACCOSMOKINGONSET              "lower yearoftobaccosmokingonset" "N=0"
> q(save="no")
