
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/472715/BLCA-TP.miRseq_RPKM_log2.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/472715/BLCA-TP.miRseq_RPKM_log2.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/472715/BLCA-TP.miRseq_RPKM_log2.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/472715/BLCA-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] "NEOPLASM.DISEASESTAGE"
[1] "PATHOLOGY.T.STAGE"
[1] "PATHOLOGY.N.STAGE"
[1] "PATHOLOGY.M.STAGE"
[1] "GENDER"
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "NUMBERPACKYEARSSMOKED"
[1] "NUMBER.OF.LYMPH.NODES"
[1] 6
                            Clinical feature             
Time to Death               "Time to Death"              
AGE                         "AGE"                        
NEOPLASM.DISEASESTAGE       "NEOPLASM DISEASESTAGE"      
PATHOLOGY.T.STAGE           "PATHOLOGY T STAGE"          
PATHOLOGY.N.STAGE           "PATHOLOGY N STAGE"          
PATHOLOGY.M.STAGE           "PATHOLOGY M STAGE"          
GENDER                      "GENDER"                     
KARNOFSKY.PERFORMANCE.SCORE "KARNOFSKY PERFORMANCE SCORE"
NUMBERPACKYEARSSMOKED       "NUMBERPACKYEARSSMOKED"      
NUMBER.OF.LYMPH.NODES       "NUMBER OF LYMPH NODES"      
                            Statistical test            Significant genes
Time to Death               "Cox regression test"       "N=0"            
AGE                         "Spearman correlation test" "N=3"            
NEOPLASM.DISEASESTAGE       "ANOVA test"                "N=0"            
PATHOLOGY.T.STAGE           "Spearman correlation test" "N=6"            
PATHOLOGY.N.STAGE           "Spearman correlation test" "N=0"            
PATHOLOGY.M.STAGE           "ANOVA test"                "N=2"            
GENDER                      "t test"                    "N=2"            
KARNOFSKY.PERFORMANCE.SCORE "Spearman correlation test" "N=0"            
NUMBERPACKYEARSSMOKED       "Spearman correlation test" "N=0"            
NUMBER.OF.LYMPH.NODES       "Spearman correlation test" "N=0"            
                            Associated with
Time to Death               " "            
AGE                         "older"        
NEOPLASM.DISEASESTAGE       " "            
PATHOLOGY.T.STAGE           "higher stage" 
PATHOLOGY.N.STAGE           " "            
PATHOLOGY.M.STAGE           " "            
GENDER                      "male"         
KARNOFSKY.PERFORMANCE.SCORE " "            
NUMBERPACKYEARSSMOKED       " "            
NUMBER.OF.LYMPH.NODES       " "            
                            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Time to Death               " "                                                                                       
AGE                         "N=3"                                                                                     
NEOPLASM.DISEASESTAGE       " "                                                                                       
PATHOLOGY.T.STAGE           "N=5"                                                                                     
PATHOLOGY.N.STAGE           " "                                                                                       
PATHOLOGY.M.STAGE           " "                                                                                       
GENDER                      "N=2"                                                                                     
KARNOFSKY.PERFORMANCE.SCORE " "                                                                                       
NUMBERPACKYEARSSMOKED       " "                                                                                       
NUMBER.OF.LYMPH.NODES       " "                                                                                       
                            Associated with      
Time to Death               " "             " "  
AGE                         "younger"       "N=0"
NEOPLASM.DISEASESTAGE       " "             " "  
PATHOLOGY.T.STAGE           "lower stage"   "N=1"
PATHOLOGY.N.STAGE           " "             " "  
PATHOLOGY.M.STAGE           " "             " "  
GENDER                      "female"        "N=0"
KARNOFSKY.PERFORMANCE.SCORE " "             " "  
NUMBERPACKYEARSSMOKED       " "             " "  
NUMBER.OF.LYMPH.NODES       " "             " "  
> q(save="no")
