
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/417615/PANCAN12-TP.medianexp.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/417615/PANCAN12-TP.medianexp.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/417615/PANCAN12-TP.medianexp.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/417615/PANCAN12-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] "PRIMARY.SITE.OF.DISEASE"
[1] "GENDER"
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "HISTOLOGICAL.TYPE"
[1] "TUMOR.STAGE"
[1] "RADIATIONS.RADIATION.REGIMENINDICATION"
[1] "NUMBERPACKYEARSSMOKED"
[1] "YEAROFTOBACCOSMOKINGONSET"
[1] "DISTANT.METASTASIS"
[1] "LYMPH.NODE.METASTASIS"
[1] "COMPLETENESS.OF.RESECTION"
[1] "NUMBER.OF.LYMPH.NODES"
[1] "NEOPLASM.DISEASESTAGE"
[1] 6
                                       Clinical feature                        
Time to Death                          "Time to Death"                         
AGE                                    "AGE"                                   
PRIMARY.SITE.OF.DISEASE                "PRIMARY SITE OF DISEASE"               
GENDER                                 "GENDER"                                
KARNOFSKY.PERFORMANCE.SCORE            "KARNOFSKY PERFORMANCE SCORE"           
HISTOLOGICAL.TYPE                      "HISTOLOGICAL TYPE"                     
TUMOR.STAGE                            "TUMOR STAGE"                           
RADIATIONS.RADIATION.REGIMENINDICATION "RADIATIONS RADIATION REGIMENINDICATION"
NUMBERPACKYEARSSMOKED                  "NUMBERPACKYEARSSMOKED"                 
YEAROFTOBACCOSMOKINGONSET              "YEAROFTOBACCOSMOKINGONSET"             
DISTANT.METASTASIS                     "DISTANT METASTASIS"                    
LYMPH.NODE.METASTASIS                  "LYMPH NODE METASTASIS"                 
COMPLETENESS.OF.RESECTION              "COMPLETENESS OF RESECTION"             
NUMBER.OF.LYMPH.NODES                  "NUMBER OF LYMPH NODES"                 
NEOPLASM.DISEASESTAGE                  "NEOPLASM DISEASESTAGE"                 
                                       Statistical test           
Time to Death                          "Cox regression test"      
AGE                                    "Spearman correlation test"
PRIMARY.SITE.OF.DISEASE                "ANOVA test"               
GENDER                                 "t test"                   
KARNOFSKY.PERFORMANCE.SCORE            "Spearman correlation test"
HISTOLOGICAL.TYPE                      "ANOVA test"               
TUMOR.STAGE                            "Spearman correlation test"
RADIATIONS.RADIATION.REGIMENINDICATION "t test"                   
NUMBERPACKYEARSSMOKED                  "Spearman correlation test"
YEAROFTOBACCOSMOKINGONSET              "Spearman correlation test"
DISTANT.METASTASIS                     "ANOVA test"               
LYMPH.NODE.METASTASIS                  "ANOVA test"               
COMPLETENESS.OF.RESECTION              "ANOVA test"               
NUMBER.OF.LYMPH.NODES                  "Spearman correlation test"
NEOPLASM.DISEASESTAGE                  "ANOVA test"               
                                       Significant genes
Time to Death                          "N=3048"         
AGE                                    "N=3682"         
PRIMARY.SITE.OF.DISEASE                "N=17229"        
GENDER                                 "N=8979"         
KARNOFSKY.PERFORMANCE.SCORE            "N=196"          
HISTOLOGICAL.TYPE                      "N=17150"        
TUMOR.STAGE                            "N=0"            
RADIATIONS.RADIATION.REGIMENINDICATION "N=5806"         
NUMBERPACKYEARSSMOKED                  "N=0"            
YEAROFTOBACCOSMOKINGONSET              "N=2"            
DISTANT.METASTASIS                     "N=576"          
LYMPH.NODE.METASTASIS                  "N=9839"         
COMPLETENESS.OF.RESECTION              "N=2084"         
NUMBER.OF.LYMPH.NODES                  "N=0"            
NEOPLASM.DISEASESTAGE                  "N=10650"        
                                       Associated with                   
Time to Death                          "shorter survival"                
AGE                                    "older"                           
PRIMARY.SITE.OF.DISEASE                " "                               
GENDER                                 "male"                            
KARNOFSKY.PERFORMANCE.SCORE            "higher score"                    
HISTOLOGICAL.TYPE                      " "                               
TUMOR.STAGE                            " "                               
RADIATIONS.RADIATION.REGIMENINDICATION "yes"                             
NUMBERPACKYEARSSMOKED                  " "                               
YEAROFTOBACCOSMOKINGONSET              "higher yearoftobaccosmokingonset"
DISTANT.METASTASIS                     " "                               
LYMPH.NODE.METASTASIS                  " "                               
COMPLETENESS.OF.RESECTION              " "                               
NUMBER.OF.LYMPH.NODES                  " "                               
NEOPLASM.DISEASESTAGE                  " "                               
                                       &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Time to Death                          "N=1442"                                                                                  
AGE                                    "N=1744"                                                                                  
PRIMARY.SITE.OF.DISEASE                " "                                                                                       
GENDER                                 "N=4341"                                                                                  
KARNOFSKY.PERFORMANCE.SCORE            "N=92"                                                                                    
HISTOLOGICAL.TYPE                      " "                                                                                       
TUMOR.STAGE                            " "                                                                                       
RADIATIONS.RADIATION.REGIMENINDICATION "N=2804"                                                                                  
NUMBERPACKYEARSSMOKED                  " "                                                                                       
YEAROFTOBACCOSMOKINGONSET              "N=0"                                                                                     
DISTANT.METASTASIS                     " "                                                                                       
LYMPH.NODE.METASTASIS                  " "                                                                                       
COMPLETENESS.OF.RESECTION              " "                                                                                       
NUMBER.OF.LYMPH.NODES                  " "                                                                                       
NEOPLASM.DISEASESTAGE                  " "                                                                                       
                                       Associated with                  
Time to Death                          "longer survival"                
AGE                                    "younger"                        
PRIMARY.SITE.OF.DISEASE                " "                              
GENDER                                 "female"                         
KARNOFSKY.PERFORMANCE.SCORE            "lower score"                    
HISTOLOGICAL.TYPE                      " "                              
TUMOR.STAGE                            " "                              
RADIATIONS.RADIATION.REGIMENINDICATION "no"                             
NUMBERPACKYEARSSMOKED                  " "                              
YEAROFTOBACCOSMOKINGONSET              "lower yearoftobaccosmokingonset"
DISTANT.METASTASIS                     " "                              
LYMPH.NODE.METASTASIS                  " "                              
COMPLETENESS.OF.RESECTION              " "                              
NUMBER.OF.LYMPH.NODES                  " "                              
NEOPLASM.DISEASESTAGE                  " "                              
                                               
Time to Death                          "N=1606"
AGE                                    "N=1938"
PRIMARY.SITE.OF.DISEASE                " "     
GENDER                                 "N=4638"
KARNOFSKY.PERFORMANCE.SCORE            "N=104" 
HISTOLOGICAL.TYPE                      " "     
TUMOR.STAGE                            " "     
RADIATIONS.RADIATION.REGIMENINDICATION "N=3002"
NUMBERPACKYEARSSMOKED                  " "     
YEAROFTOBACCOSMOKINGONSET              "N=2"   
DISTANT.METASTASIS                     " "     
LYMPH.NODE.METASTASIS                  " "     
COMPLETENESS.OF.RESECTION              " "     
NUMBER.OF.LYMPH.NODES                  " "     
NEOPLASM.DISEASESTAGE                  " "     
> q(save="no")
