
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/403951/SKCM-All_Primary.rppa.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/403951/SKCM-All_Primary.rppa.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/403951/SKCM-All_Primary.rppa.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/403951/SKCM-All_Primary.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] "Time to Death"
[1] "AGE"
[1] "PRIMARY.SITE.OF.DISEASE"
[1] "LYMPH.NODE.METASTASIS"
[1] "NEOPLASM.DISEASESTAGE"
[1] 6
                        Clinical feature          Statistical test           
Time to Death           "Time to Death"           "Cox regression test"      
AGE                     "AGE"                     "Spearman correlation test"
PRIMARY.SITE.OF.DISEASE "PRIMARY SITE OF DISEASE" "ANOVA test"               
LYMPH.NODE.METASTASIS   "LYMPH NODE METASTASIS"   "ANOVA test"               
NEOPLASM.DISEASESTAGE   "NEOPLASM DISEASESTAGE"   "ANOVA test"               
                        Significant genes Associated with
Time to Death           "N=0"             " "            
AGE                     "N=1"             "older"        
PRIMARY.SITE.OF.DISEASE "N=0"             " "            
LYMPH.NODE.METASTASIS   "N=0"             " "            
NEOPLASM.DISEASESTAGE   "N=0"             " "            
                        &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Time to Death           " "                                                                                       
AGE                     "N=0"                                                                                     
PRIMARY.SITE.OF.DISEASE " "                                                                                       
LYMPH.NODE.METASTASIS   " "                                                                                       
NEOPLASM.DISEASESTAGE   " "                                                                                       
                        Associated with      
Time to Death           " "             " "  
AGE                     "younger"       "N=1"
PRIMARY.SITE.OF.DISEASE " "             " "  
LYMPH.NODE.METASTASIS   " "             " "  
NEOPLASM.DISEASESTAGE   " "             " "  
> q(save="no")
