
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/443787/THCA-HistologicalType_Follicular.rppa.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/443787/THCA-HistologicalType_Follicular.rppa.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/443787/THCA-HistologicalType_Follicular.rppa.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/443787/THCA-HistologicalType_Follicular.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] "AGE"
[1] "GENDER"
[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"                   
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            Significant genes
AGE                       "Spearman correlation test" "N=0"            
GENDER                    "t test"                    "N=0"            
RADIATIONEXPOSURE         "t test"                    "N=1"            
DISTANT.METASTASIS        "ANOVA test"                "N=0"            
EXTRATHYROIDAL.EXTENSION  "ANOVA test"                "N=0"            
LYMPH.NODE.METASTASIS     "ANOVA test"                "N=0"            
COMPLETENESS.OF.RESECTION "ANOVA test"                "N=0"            
NUMBER.OF.LYMPH.NODES     "Spearman correlation test" "N=0"            
NEOPLASM.DISEASESTAGE     "ANOVA test"                "N=1"            
MULTIFOCALITY             "t test"                    "N=0"            
TUMOR.SIZE                "Spearman correlation test" "N=0"            
                          Associated with
AGE                       " "            
GENDER                    " "            
RADIATIONEXPOSURE         "yes"          
DISTANT.METASTASIS        " "            
EXTRATHYROIDAL.EXTENSION  " "            
LYMPH.NODE.METASTASIS     " "            
COMPLETENESS.OF.RESECTION " "            
NUMBER.OF.LYMPH.NODES     " "            
NEOPLASM.DISEASESTAGE     " "            
MULTIFOCALITY             " "            
TUMOR.SIZE                " "            
                          &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
AGE                       " "                                                                                       
GENDER                    " "                                                                                       
RADIATIONEXPOSURE         "N=0"                                                                                     
DISTANT.METASTASIS        " "                                                                                       
EXTRATHYROIDAL.EXTENSION  " "                                                                                       
LYMPH.NODE.METASTASIS     " "                                                                                       
COMPLETENESS.OF.RESECTION " "                                                                                       
NUMBER.OF.LYMPH.NODES     " "                                                                                       
NEOPLASM.DISEASESTAGE     " "                                                                                       
MULTIFOCALITY             " "                                                                                       
TUMOR.SIZE                " "                                                                                       
                          Associated with      
AGE                       " "             " "  
GENDER                    " "             " "  
RADIATIONEXPOSURE         "no"            "N=1"
DISTANT.METASTASIS        " "             " "  
EXTRATHYROIDAL.EXTENSION  " "             " "  
LYMPH.NODE.METASTASIS     " "             " "  
COMPLETENESS.OF.RESECTION " "             " "  
NUMBER.OF.LYMPH.NODES     " "             " "  
NEOPLASM.DISEASESTAGE     " "             " "  
MULTIFOCALITY             " "             " "  
TUMOR.SIZE                " "             " "  
> q(save="no")
