
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/373496/THCA-TP.meth.for_correlation.filtered_data.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/373496/THCA-TP.meth.for_correlation.filtered_data.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/373496/THCA-TP.meth.for_correlation.filtered_data.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/373496/THCA-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] "AGE"
[1] "GENDER"
[1] "HISTOLOGICAL.TYPE"
[1] "RADIATIONS.RADIATION.REGIMENINDICATION"
[1] "RADIATIONEXPOSURE"
[1] "DISTANT.METASTASIS"
[1] "EXTRATHYROIDAL.EXTENSION"
[1] "LYMPH.NODE.METASTASIS"
[1] "COMPLETENESS.OF.RESECTION"
[1] "NUMBER.OF.LYMPH.NODES"
[1] "NEOPLASM.DISEASESTAGE"
[1] "MULTIFOCALITY"
[1] "TUMOR.SIZE"
[1] 6
                                       Clinical feature                        
AGE                                    "AGE"                                   
GENDER                                 "GENDER"                                
HISTOLOGICAL.TYPE                      "HISTOLOGICAL TYPE"                     
RADIATIONS.RADIATION.REGIMENINDICATION "RADIATIONS RADIATION REGIMENINDICATION"
RADIATIONEXPOSURE                      "RADIATIONEXPOSURE"                     
DISTANT.METASTASIS                     "DISTANT METASTASIS"                    
EXTRATHYROIDAL.EXTENSION               "EXTRATHYROIDAL EXTENSION"              
LYMPH.NODE.METASTASIS                  "LYMPH NODE METASTASIS"                 
COMPLETENESS.OF.RESECTION              "COMPLETENESS OF RESECTION"             
NUMBER.OF.LYMPH.NODES                  "NUMBER OF LYMPH NODES"                 
NEOPLASM.DISEASESTAGE                  "NEOPLASM DISEASESTAGE"                 
MULTIFOCALITY                          "MULTIFOCALITY"                         
TUMOR.SIZE                             "TUMOR SIZE"                            
                                       Statistical test           
AGE                                    "Spearman correlation test"
GENDER                                 "t test"                   
HISTOLOGICAL.TYPE                      "ANOVA test"               
RADIATIONS.RADIATION.REGIMENINDICATION "t test"                   
RADIATIONEXPOSURE                      "t test"                   
DISTANT.METASTASIS                     "ANOVA test"               
EXTRATHYROIDAL.EXTENSION               "ANOVA test"               
LYMPH.NODE.METASTASIS                  "ANOVA test"               
COMPLETENESS.OF.RESECTION              "ANOVA test"               
NUMBER.OF.LYMPH.NODES                  "Spearman correlation test"
NEOPLASM.DISEASESTAGE                  "ANOVA test"               
MULTIFOCALITY                          "t test"                   
TUMOR.SIZE                             "Spearman correlation test"
                                       Significant genes
AGE                                    "N=159"          
GENDER                                 "N=11"           
HISTOLOGICAL.TYPE                      "N=1855"         
RADIATIONS.RADIATION.REGIMENINDICATION "N=38"           
RADIATIONEXPOSURE                      "N=24"           
DISTANT.METASTASIS                     "N=33"           
EXTRATHYROIDAL.EXTENSION               "N=33"           
LYMPH.NODE.METASTASIS                  "N=396"          
COMPLETENESS.OF.RESECTION              "N=20"           
NUMBER.OF.LYMPH.NODES                  "N=618"          
NEOPLASM.DISEASESTAGE                  "N=92"           
MULTIFOCALITY                          "N=0"            
TUMOR.SIZE                             "N=3"            
                                       Associated with               
AGE                                    "older"                       
GENDER                                 "male"                        
HISTOLOGICAL.TYPE                      " "                           
RADIATIONS.RADIATION.REGIMENINDICATION "yes"                         
RADIATIONEXPOSURE                      "yes"                         
DISTANT.METASTASIS                     " "                           
EXTRATHYROIDAL.EXTENSION               " "                           
LYMPH.NODE.METASTASIS                  " "                           
COMPLETENESS.OF.RESECTION              " "                           
NUMBER.OF.LYMPH.NODES                  "higher number.of.lymph.nodes"
NEOPLASM.DISEASESTAGE                  " "                           
MULTIFOCALITY                          " "                           
TUMOR.SIZE                             "higher tumor.size"           
                                       &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
AGE                                    "N=158"                                                                                   
GENDER                                 "N=5"                                                                                     
HISTOLOGICAL.TYPE                      " "                                                                                       
RADIATIONS.RADIATION.REGIMENINDICATION "N=23"                                                                                    
RADIATIONEXPOSURE                      "N=11"                                                                                    
DISTANT.METASTASIS                     " "                                                                                       
EXTRATHYROIDAL.EXTENSION               " "                                                                                       
LYMPH.NODE.METASTASIS                  " "                                                                                       
COMPLETENESS.OF.RESECTION              " "                                                                                       
NUMBER.OF.LYMPH.NODES                  "N=13"                                                                                    
NEOPLASM.DISEASESTAGE                  " "                                                                                       
MULTIFOCALITY                          " "                                                                                       
TUMOR.SIZE                             "N=3"                                                                                     
                                       Associated with                      
AGE                                    "younger"                     "N=1"  
GENDER                                 "female"                      "N=6"  
HISTOLOGICAL.TYPE                      " "                           " "    
RADIATIONS.RADIATION.REGIMENINDICATION "no"                          "N=15" 
RADIATIONEXPOSURE                      "no"                          "N=13" 
DISTANT.METASTASIS                     " "                           " "    
EXTRATHYROIDAL.EXTENSION               " "                           " "    
LYMPH.NODE.METASTASIS                  " "                           " "    
COMPLETENESS.OF.RESECTION              " "                           " "    
NUMBER.OF.LYMPH.NODES                  "lower number.of.lymph.nodes" "N=605"
NEOPLASM.DISEASESTAGE                  " "                           " "    
MULTIFOCALITY                          " "                           " "    
TUMOR.SIZE                             "lower tumor.size"            "N=0"  
> q(save="no")
