
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/479481/PAAD-TP.meth.by_min_expr_corr.data.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/479481/PAAD-TP.meth.by_min_expr_corr.data.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/479481/PAAD-TP.meth.by_min_expr_corr.data.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/479481/PAAD-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] "HISTOLOGICAL.TYPE"
[1] "NUMBERPACKYEARSSMOKED"
[1] "YEAROFTOBACCOSMOKINGONSET"
[1] "COMPLETENESS.OF.RESECTION"
[1] "NUMBER.OF.LYMPH.NODES"
[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"                   
HISTOLOGICAL.TYPE         "HISTOLOGICAL TYPE"        
NUMBERPACKYEARSSMOKED     "NUMBERPACKYEARSSMOKED"    
YEAROFTOBACCOSMOKINGONSET "YEAROFTOBACCOSMOKINGONSET"
COMPLETENESS.OF.RESECTION "COMPLETENESS OF RESECTION"
NUMBER.OF.LYMPH.NODES     "NUMBER OF LYMPH NODES"    
                          Statistical test            Significant genes
Time to Death             "Cox regression test"       "N=0"            
AGE                       "Spearman correlation test" "N=0"            
NEOPLASM.DISEASESTAGE     "ANOVA test"                "N=7"            
PATHOLOGY.T.STAGE         "Spearman correlation test" "N=0"            
PATHOLOGY.N.STAGE         "t test"                    "N=0"            
PATHOLOGY.M.STAGE         "ANOVA test"                "N=16"           
GENDER                    "t test"                    "N=6"            
HISTOLOGICAL.TYPE         "ANOVA test"                "N=14"           
NUMBERPACKYEARSSMOKED     "Spearman correlation test" "N=0"            
YEAROFTOBACCOSMOKINGONSET "Spearman correlation test" "N=1"            
COMPLETENESS.OF.RESECTION "ANOVA test"                "N=118"          
NUMBER.OF.LYMPH.NODES     "Spearman correlation test" "N=0"            
                          Associated with                   
Time to Death             " "                               
AGE                       " "                               
NEOPLASM.DISEASESTAGE     " "                               
PATHOLOGY.T.STAGE         " "                               
PATHOLOGY.N.STAGE         " "                               
PATHOLOGY.M.STAGE         " "                               
GENDER                    "male"                            
HISTOLOGICAL.TYPE         " "                               
NUMBERPACKYEARSSMOKED     " "                               
YEAROFTOBACCOSMOKINGONSET "higher yearoftobaccosmokingonset"
COMPLETENESS.OF.RESECTION " "                               
NUMBER.OF.LYMPH.NODES     " "                               
                          &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         " "                                                                                       
GENDER                    "N=4"                                                                                     
HISTOLOGICAL.TYPE         " "                                                                                       
NUMBERPACKYEARSSMOKED     " "                                                                                       
YEAROFTOBACCOSMOKINGONSET "N=1"                                                                                     
COMPLETENESS.OF.RESECTION " "                                                                                       
NUMBER.OF.LYMPH.NODES     " "                                                                                       
                          Associated with                        
Time to Death             " "                               " "  
AGE                       " "                               " "  
NEOPLASM.DISEASESTAGE     " "                               " "  
PATHOLOGY.T.STAGE         " "                               " "  
PATHOLOGY.N.STAGE         " "                               " "  
PATHOLOGY.M.STAGE         " "                               " "  
GENDER                    "female"                          "N=2"
HISTOLOGICAL.TYPE         " "                               " "  
NUMBERPACKYEARSSMOKED     " "                               " "  
YEAROFTOBACCOSMOKINGONSET "lower yearoftobaccosmokingonset" "N=0"
COMPLETENESS.OF.RESECTION " "                               " "  
NUMBER.OF.LYMPH.NODES     " "                               " "  
> q(save="no")
