
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/416140/READ-TP.uncv2.mRNAseq_RSEM_normalized_log2.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/416140/READ-TP.uncv2.mRNAseq_RSEM_normalized_log2.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/416140/READ-TP.uncv2.mRNAseq_RSEM_normalized_log2.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/416140/READ-TP.clin.merged.picked.clindata.txt", "-cP=1", "-cQ=0.05", "-nV=Nozzle.R1", "-OP=MRNASEQ_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] "RADIATIONS.RADIATION.REGIMENINDICATION"
[1] "DISTANT.METASTASIS"
[1] "LYMPH.NODE.METASTASIS"
[1] "COMPLETENESS.OF.RESECTION"
[1] "NUMBER.OF.LYMPH.NODES"
[1] "NEOPLASM.DISEASESTAGE"
[1] 6
                                       Clinical feature                        
AGE                                    "AGE"                                   
GENDER                                 "GENDER"                                
RADIATIONS.RADIATION.REGIMENINDICATION "RADIATIONS RADIATION REGIMENINDICATION"
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           
AGE                                    "Spearman correlation test"
GENDER                                 "t test"                   
RADIATIONS.RADIATION.REGIMENINDICATION "t 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 Associated with
AGE                                    "N=0"             " "            
GENDER                                 "N=14"            "male"         
RADIATIONS.RADIATION.REGIMENINDICATION "N=47"            "yes"          
DISTANT.METASTASIS                     "N=0"             " "            
LYMPH.NODE.METASTASIS                  "N=0"             " "            
COMPLETENESS.OF.RESECTION              "N=0"             " "            
NUMBER.OF.LYMPH.NODES                  "N=0"             " "            
NEOPLASM.DISEASESTAGE                  "N=2"             " "            
                                       &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
AGE                                    " "                                                                                       
GENDER                                 "N=12"                                                                                    
RADIATIONS.RADIATION.REGIMENINDICATION "N=15"                                                                                    
DISTANT.METASTASIS                     " "                                                                                       
LYMPH.NODE.METASTASIS                  " "                                                                                       
COMPLETENESS.OF.RESECTION              " "                                                                                       
NUMBER.OF.LYMPH.NODES                  " "                                                                                       
NEOPLASM.DISEASESTAGE                  " "                                                                                       
                                       Associated with       
AGE                                    " "             " "   
GENDER                                 "female"        "N=2" 
RADIATIONS.RADIATION.REGIMENINDICATION "no"            "N=32"
DISTANT.METASTASIS                     " "             " "   
LYMPH.NODE.METASTASIS                  " "             " "   
COMPLETENESS.OF.RESECTION              " "             " "   
NUMBER.OF.LYMPH.NODES                  " "             " "   
NEOPLASM.DISEASESTAGE                  " "             " "   
> q(save="no")
