
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/474125/LUSC-TP.medianexp.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/474125/LUSC-TP.medianexp.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/474125/LUSC-TP.medianexp.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/474125/LUSC-TP.clin.merged.picked.clindata.txt", "-cP=1", "-cQ=0.05", "-nV=Nozzle.R1", "-OP=MRNA_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] "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"          
NUMBERPACKYEARSSMOKED       "NUMBERPACKYEARSSMOKED"      
YEAROFTOBACCOSMOKINGONSET   "YEAROFTOBACCOSMOKINGONSET"  
COMPLETENESS.OF.RESECTION   "COMPLETENESS OF RESECTION"  
                            Statistical test            Significant genes
Time to Death               "Cox regression test"       "N=0"            
AGE                         "Spearman correlation test" "N=0"            
NEOPLASM.DISEASESTAGE       "ANOVA test"                "N=0"            
PATHOLOGY.T.STAGE           "Spearman correlation test" "N=0"            
PATHOLOGY.N.STAGE           "Spearman correlation test" "N=0"            
PATHOLOGY.M.STAGE           "t test"                    "N=20"           
GENDER                      "t test"                    "N=13"           
KARNOFSKY.PERFORMANCE.SCORE "Spearman correlation test" "N=0"            
HISTOLOGICAL.TYPE           "ANOVA test"                "N=13"           
NUMBERPACKYEARSSMOKED       "Spearman correlation test" "N=0"            
YEAROFTOBACCOSMOKINGONSET   "Spearman correlation test" "N=0"            
COMPLETENESS.OF.RESECTION   "ANOVA test"                "N=2"            
                            Associated with
Time to Death               " "            
AGE                         " "            
NEOPLASM.DISEASESTAGE       " "            
PATHOLOGY.T.STAGE           " "            
PATHOLOGY.N.STAGE           " "            
PATHOLOGY.M.STAGE           "m1"           
GENDER                      "male"         
KARNOFSKY.PERFORMANCE.SCORE " "            
HISTOLOGICAL.TYPE           " "            
NUMBERPACKYEARSSMOKED       " "            
YEAROFTOBACCOSMOKINGONSET   " "            
COMPLETENESS.OF.RESECTION   " "            
                            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Time to Death               " "                                                                                       
AGE                         " "                                                                                       
NEOPLASM.DISEASESTAGE       " "                                                                                       
PATHOLOGY.T.STAGE           " "                                                                                       
PATHOLOGY.N.STAGE           " "                                                                                       
PATHOLOGY.M.STAGE           "N=4"                                                                                     
GENDER                      "N=13"                                                                                    
KARNOFSKY.PERFORMANCE.SCORE " "                                                                                       
HISTOLOGICAL.TYPE           " "                                                                                       
NUMBERPACKYEARSSMOKED       " "                                                                                       
YEAROFTOBACCOSMOKINGONSET   " "                                                                                       
COMPLETENESS.OF.RESECTION   " "                                                                                       
                            Associated with       
Time to Death               " "             " "   
AGE                         " "             " "   
NEOPLASM.DISEASESTAGE       " "             " "   
PATHOLOGY.T.STAGE           " "             " "   
PATHOLOGY.N.STAGE           " "             " "   
PATHOLOGY.M.STAGE           "m0"            "N=16"
GENDER                      "female"        "N=0" 
KARNOFSKY.PERFORMANCE.SCORE " "             " "   
HISTOLOGICAL.TYPE           " "             " "   
NUMBERPACKYEARSSMOKED       " "             " "   
YEAROFTOBACCOSMOKINGONSET   " "             " "   
COMPLETENESS.OF.RESECTION   " "             " "   
> q(save="no")
