
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/474050/LUSC-TP.rppa.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/474050/LUSC-TP.rppa.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/474050/LUSC-TP.rppa.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/474050/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] "NEOPLASM.DISEASESTAGE"
[1] "PATHOLOGY.T.STAGE"
[1] "PATHOLOGY.N.STAGE"
[1] "PATHOLOGY.M.STAGE"
[1] "GENDER"
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "HISTOLOGICAL.TYPE"
[1] "RADIATIONS.RADIATION.REGIMENINDICATION"
[1] "NUMBERPACKYEARSSMOKED"
[1] "YEAROFTOBACCOSMOKINGONSET"
[1] "COMPLETENESS.OF.RESECTION"
[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"           
HISTOLOGICAL.TYPE                      "HISTOLOGICAL TYPE"                     
RADIATIONS.RADIATION.REGIMENINDICATION "RADIATIONS RADIATION REGIMENINDICATION"
NUMBERPACKYEARSSMOKED                  "NUMBERPACKYEARSSMOKED"                 
YEAROFTOBACCOSMOKINGONSET              "YEAROFTOBACCOSMOKINGONSET"             
COMPLETENESS.OF.RESECTION              "COMPLETENESS OF RESECTION"             
                                       Statistical test           
Time to Death                          "Cox regression test"      
AGE                                    "Spearman correlation test"
NEOPLASM.DISEASESTAGE                  "ANOVA test"               
PATHOLOGY.T.STAGE                      "Spearman correlation test"
PATHOLOGY.N.STAGE                      "Spearman correlation test"
PATHOLOGY.M.STAGE                      "t test"                   
GENDER                                 "t test"                   
KARNOFSKY.PERFORMANCE.SCORE            "Spearman correlation test"
HISTOLOGICAL.TYPE                      "ANOVA test"               
RADIATIONS.RADIATION.REGIMENINDICATION "t test"                   
NUMBERPACKYEARSSMOKED                  "Spearman correlation test"
YEAROFTOBACCOSMOKINGONSET              "Spearman correlation test"
COMPLETENESS.OF.RESECTION              "ANOVA test"               
                                       Significant genes
Time to Death                          "N=0"            
AGE                                    "N=2"            
NEOPLASM.DISEASESTAGE                  "N=1"            
PATHOLOGY.T.STAGE                      "N=2"            
PATHOLOGY.N.STAGE                      "N=2"            
PATHOLOGY.M.STAGE                      "N=0"            
GENDER                                 "N=0"            
KARNOFSKY.PERFORMANCE.SCORE            "N=0"            
HISTOLOGICAL.TYPE                      "N=4"            
RADIATIONS.RADIATION.REGIMENINDICATION "N=0"            
NUMBERPACKYEARSSMOKED                  "N=0"            
YEAROFTOBACCOSMOKINGONSET              "N=1"            
COMPLETENESS.OF.RESECTION              "N=2"            
                                       Associated with                   
Time to Death                          " "                               
AGE                                    "older"                           
NEOPLASM.DISEASESTAGE                  " "                               
PATHOLOGY.T.STAGE                      "higher stage"                    
PATHOLOGY.N.STAGE                      "higher stage"                    
PATHOLOGY.M.STAGE                      " "                               
GENDER                                 " "                               
KARNOFSKY.PERFORMANCE.SCORE            " "                               
HISTOLOGICAL.TYPE                      " "                               
RADIATIONS.RADIATION.REGIMENINDICATION " "                               
NUMBERPACKYEARSSMOKED                  " "                               
YEAROFTOBACCOSMOKINGONSET              "higher yearoftobaccosmokingonset"
COMPLETENESS.OF.RESECTION              " "                               
                                       &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                      "N=2"                                                                                     
PATHOLOGY.N.STAGE                      "N=0"                                                                                     
PATHOLOGY.M.STAGE                      " "                                                                                       
GENDER                                 " "                                                                                       
KARNOFSKY.PERFORMANCE.SCORE            " "                                                                                       
HISTOLOGICAL.TYPE                      " "                                                                                       
RADIATIONS.RADIATION.REGIMENINDICATION " "                                                                                       
NUMBERPACKYEARSSMOKED                  " "                                                                                       
YEAROFTOBACCOSMOKINGONSET              "N=1"                                                                                     
COMPLETENESS.OF.RESECTION              " "                                                                                       
                                       Associated with                        
Time to Death                          " "                               " "  
AGE                                    "younger"                         "N=2"
NEOPLASM.DISEASESTAGE                  " "                               " "  
PATHOLOGY.T.STAGE                      "lower stage"                     "N=0"
PATHOLOGY.N.STAGE                      "lower stage"                     "N=2"
PATHOLOGY.M.STAGE                      " "                               " "  
GENDER                                 " "                               " "  
KARNOFSKY.PERFORMANCE.SCORE            " "                               " "  
HISTOLOGICAL.TYPE                      " "                               " "  
RADIATIONS.RADIATION.REGIMENINDICATION " "                               " "  
NUMBERPACKYEARSSMOKED                  " "                               " "  
YEAROFTOBACCOSMOKINGONSET              "lower yearoftobaccosmokingonset" "N=0"
COMPLETENESS.OF.RESECTION              " "                               " "  
> q(save="no")
