
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/299289/LGG-TP.miRseq_RPKM_log2.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/299289/LGG-TP.miRseq_RPKM_log2.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/299289/LGG-TP.miRseq_RPKM_log2.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/299289/LGG-TP.clin.merged.picked.clindata.txt", "-cP=1", "-cQ=0.05", "-nV=Nozzle.R1", "-OP=MIRNASEQ_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] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "HISTOLOGICAL.TYPE"
[1] "RADIATIONS.RADIATION.REGIMENINDICATION"
[1] 6
                                       Clinical feature                        
Time to Death                          "Time to Death"                         
AGE                                    "AGE"                                   
GENDER                                 "GENDER"                                
KARNOFSKY.PERFORMANCE.SCORE            "KARNOFSKY PERFORMANCE SCORE"           
HISTOLOGICAL.TYPE                      "HISTOLOGICAL TYPE"                     
RADIATIONS.RADIATION.REGIMENINDICATION "RADIATIONS RADIATION REGIMENINDICATION"
                                       Statistical test           
Time to Death                          "Cox regression test"      
AGE                                    "Spearman correlation test"
GENDER                                 "t test"                   
KARNOFSKY.PERFORMANCE.SCORE            "Spearman correlation test"
HISTOLOGICAL.TYPE                      "ANOVA test"               
RADIATIONS.RADIATION.REGIMENINDICATION "t test"                   
                                       Significant genes Associated with   
Time to Death                          "N=6"             "shorter survival"
AGE                                    "N=1"             "older"           
GENDER                                 "N=0"             " "               
KARNOFSKY.PERFORMANCE.SCORE            "N=0"             " "               
HISTOLOGICAL.TYPE                      "N=29"            " "               
RADIATIONS.RADIATION.REGIMENINDICATION "N=1"             "yes"             
                                       &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Time to Death                          "N=5"                                                                                     
AGE                                    "N=1"                                                                                     
GENDER                                 " "                                                                                       
KARNOFSKY.PERFORMANCE.SCORE            " "                                                                                       
HISTOLOGICAL.TYPE                      " "                                                                                       
RADIATIONS.RADIATION.REGIMENINDICATION "N=0"                                                                                     
                                       Associated with        
Time to Death                          "longer survival" "N=1"
AGE                                    "younger"         "N=0"
GENDER                                 " "               " "  
KARNOFSKY.PERFORMANCE.SCORE            " "               " "  
HISTOLOGICAL.TYPE                      " "               " "  
RADIATIONS.RADIATION.REGIMENINDICATION "no"              "N=1"
> q(save="no")
