
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/394792/BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/394792/BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/394792/BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/394792/BRCA-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] "Time to Death"
[1] "AGE"
[1] "GENDER"
[1] "RADIATIONS.RADIATION.REGIMENINDICATION"
[1] "DISTANT.METASTASIS"
[1] "LYMPH.NODE.METASTASIS"
[1] "NUMBER.OF.LYMPH.NODES"
[1] "NEOPLASM.DISEASESTAGE"
[1] 6
                                       Clinical feature                        
Time to Death                          "Time to Death"                         
AGE                                    "AGE"                                   
GENDER                                 "GENDER"                                
RADIATIONS.RADIATION.REGIMENINDICATION "RADIATIONS RADIATION REGIMENINDICATION"
DISTANT.METASTASIS                     "DISTANT METASTASIS"                    
LYMPH.NODE.METASTASIS                  "LYMPH NODE METASTASIS"                 
NUMBER.OF.LYMPH.NODES                  "NUMBER OF LYMPH NODES"                 
NEOPLASM.DISEASESTAGE                  "NEOPLASM DISEASESTAGE"                 
                                       Statistical test           
Time to Death                          "Cox regression test"      
AGE                                    "Spearman correlation test"
GENDER                                 "t test"                   
RADIATIONS.RADIATION.REGIMENINDICATION "t test"                   
DISTANT.METASTASIS                     "ANOVA test"               
LYMPH.NODE.METASTASIS                  "ANOVA test"               
NUMBER.OF.LYMPH.NODES                  "Spearman correlation test"
NEOPLASM.DISEASESTAGE                  "ANOVA test"               
                                       Significant genes
Time to Death                          "N=4"            
AGE                                    "N=677"          
GENDER                                 "N=18"           
RADIATIONS.RADIATION.REGIMENINDICATION "N=0"            
DISTANT.METASTASIS                     "N=0"            
LYMPH.NODE.METASTASIS                  "N=8"            
NUMBER.OF.LYMPH.NODES                  "N=2"            
NEOPLASM.DISEASESTAGE                  "N=0"            
                                       Associated with               
Time to Death                          "shorter survival"            
AGE                                    "older"                       
GENDER                                 "male"                        
RADIATIONS.RADIATION.REGIMENINDICATION " "                           
DISTANT.METASTASIS                     " "                           
LYMPH.NODE.METASTASIS                  " "                           
NUMBER.OF.LYMPH.NODES                  "higher 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=3"                                                                                     
AGE                                    "N=160"                                                                                   
GENDER                                 "N=8"                                                                                     
RADIATIONS.RADIATION.REGIMENINDICATION " "                                                                                       
DISTANT.METASTASIS                     " "                                                                                       
LYMPH.NODE.METASTASIS                  " "                                                                                       
NUMBER.OF.LYMPH.NODES                  "N=1"                                                                                     
NEOPLASM.DISEASESTAGE                  " "                                                                                       
                                       Associated with                      
Time to Death                          "longer survival"             "N=1"  
AGE                                    "younger"                     "N=517"
GENDER                                 "female"                      "N=10" 
RADIATIONS.RADIATION.REGIMENINDICATION " "                           " "    
DISTANT.METASTASIS                     " "                           " "    
LYMPH.NODE.METASTASIS                  " "                           " "    
NUMBER.OF.LYMPH.NODES                  "lower number.of.lymph.nodes" "N=1"  
NEOPLASM.DISEASESTAGE                  " "                           " "    
> q(save="no")
