[1] "libdir: /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/ClinicalAnalysisAllGenes_new/broadinstitute.org/cancer.genome.analysis/00333/58/"
[1] "terrence_modification_tag: TRUE"
[1] "op: "
[1] "dfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/UCEC-TP/9831167/UCEC-TP.medianexp.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/UCEC-TP/10006384/UCEC-TP.merged_data.txt"
[1] "gv: ALL"
[1] "gfn: "
[1] "sfn: "
[1] "fv: ALL"
[1] "ofn: "
[1] "dx: "
[1] "cfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/UCEC-TP/10006384/UCEC-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=497, in expression file=54, common to both=54
Number of genes in original expression dataset=17814
[1] "ALL"
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 54 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-A5-A0G2 TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GE 
        4549         1428         1126           NA          997         3205 
TCGA-A5-A0GH TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GU TCGA-AP-A051 TCGA-AP-A052 
        2254         1841         1416          860         2545           NA 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
         181           NA         2618         1199         1758         1385 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
        1122          239          636           NA         3815         3589 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LN TCGA-AP-A0LT TCGA-AP-A0LV 
        1921           NA          965         2510         1497          763 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
          NA          603          903         2079         2191         1413 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06F 
        1075         1399         2025         1064         1640         1554 
TCGA-AX-A06J TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-B5-A0JR TCGA-B5-A0JZ TCGA-B5-A0K0 
         913         1149         2004         1731          871          862 
TCGA-B5-A0K1 TCGA-B5-A0K4 TCGA-BG-A0LW TCGA-BG-A0MI TCGA-BK-A0C9 TCGA-BK-A0CC 
         928          544          566           NA         1092          311 
Variable 1:'AGE':	nDistinctValues=32,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=47,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "HISTOLOGICAL.TYPE"                     
[3] "RADIATIONS.RADIATION.REGIMENINDICATION"
[4] "COMPLETENESS.OF.RESECTION"             
[5] "RACE"                                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 54 columns, 1 survival variables, and 5 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=32, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
