[1] "libdir: /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/ClinicalAnalysisAllGenes_new/broadinstitute.org/cancer.genome.analysis/00333/60/"
[1] "terrence_modification_tag: TRUE"
[1] "op: "
[1] "dfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/miRseq_preprocessor/SARC-TP/11489841/SARC-TP.miRseq_RPKM_log2.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/SARC-TP/11541674/SARC-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/SARC-TP/11541674/SARC-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=157, in expression file=259, common to both=155
Number of genes in original expression dataset=509
[1] "ALL"
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "DCCUPLOADDATE"                         
 [6] "GENDER"                                
 [7] "RADIATIONTHERAPY"                      
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "RACE"                                  
[10] "ETHNICITY"                             
[11] "BATCHNUMBER"                           

Input Data has 11 rows and 155 columns.

[1] "Batch" "11"   
[1] "Last Follow UP"
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
          NA           62         1163           NA         1116           NA 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
        1420         1802          960         1294         2271           NA 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
          NA           NA           NA           NA         1834          261 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
          NA         1809         1666           NA          702         2144 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
        3289          520          610          458          540         1301 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
          NA           NA           NA         1352         1197          876 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
          NA         1952           NA          587           NA          373 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
         828          455          805         2212          763          380 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
         349         2009          713          881           63          541 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A7EF 
         658           NA           NA         2017          716           NA 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS 
        1006         1085          801           NA           NA           14 
TCGA-FX-A3NJ TCGA-FX-A3NK TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
           3           NA            2          618            2            2 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
         818           NA          126           NA          729            3 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
         298           NA          650          272           98           42 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
         217           NA           NA          966           NA         4362 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
        3555           NA         2229           NA          688          191 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-KF-A41W 
          NA           NA         2181         1107          830          356 
TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
         160          118           72           15          173          136 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
         337          476            3          124         2297           NA 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N 
          NA           NA           NA           NA          153          236 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
          56           NA           NA           NA          553          639 
TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 
        5324         2841         1688           NA           22           NA 
TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ 
         200          154          402           22           NA           NA 
TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WK-A8Y0 
        2212           NA           NA           NA           NA           NA 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
        1548          525           NA          826          259          476 
TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
         254          996          749          329          376 
Variable 1:'AGE':	nDistinctValues=54,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=50,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=99,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'BATCH.NUMBER':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"    "GENDER" "RACE"  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 155 columns, 1 survival variables, and 3 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=54, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
