[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/mRNAseq_preprocessor/UCEC-TP/9831132/UCEC-TP.uncv2.mRNAseq_RSEM_normalized_log2.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=527, common to both=488
Number of genes in original expression dataset=18555
[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 488 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
          NA         4549         1428         1126         2540           NA 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
         997           98         3205         2656         2254         1750 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
        2000         1841         1841         1416         1167         1120 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
         860          633          706         2088          607          535 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ 
         596          749          884          364         1288          485 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 
         241          348         1105          292          244         2769 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
        1409           NA          162          157          223          455 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM 
          36           33           60           12          602           26 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BH 
          73           92           15           34           23           NA 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
          68           51           NA          446          684          677 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
          39           28         1125          628           41          475 
TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW 
          23           59          485           57          513           52 
TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
          71         2545           NA          181           NA         2618 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
         250         1199         1758         1385         1122          239 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
         371          636           NA         3815         3589         3357 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
         103         1921           NA         2972          965         2554 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LS TCGA-AP-A0LT 
         825         2510           NA         1875         1918         1497 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
         763         2180         1836         1700          952           NA 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
        1276         1495          204          940          317          847 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
         494          555         1026           17           NA          603 
TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
         903         2191         1413         1075         1399         2025 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
        1064         1640           NA         1554          833          913 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
        1845         1065          868         1149         1333         1220 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
        2004          404          584          516          412          464 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
         617          378          610         2337         2207         1646 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 
        2053          764         1107          337           NA           NA 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
        2167         1020         1861         2090         1016         1232 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
         589          801          540          831           NA           NA 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
        1177            7            3           10            4            6 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
          NA            1            4           NA            7           36 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0JT 
         254          440            4         2445         1422         1312 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
        1483         1237         1360          990          871          862 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
         928          788          700          544          418          520 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
         543          335          125          265         5651         3448 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11M TCGA-B5-A11N 
        2687         2303         1656         1396         1362         1337 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
        1232         1120          976         1019          832          509 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
         595          593          596          560          528          504 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
        5835           NA           NA          438          447          356 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC 
          NA          465          389         1890          153         1249 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
        1038         1063          566          614          588          637 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
        1071         1064          241         1167         1110          860 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MH TCGA-BG-A0MI TCGA-BG-A0MK 
          NA         1263         1477         1341           NA           NA 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
        1309         1196          937          644          617          469 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
         742          811          497         1043          868         1607 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
        1721          451          382          419          448          426 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
         470          470          434           55          291         1085 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
         721          612          344          207         1092         1064 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
         189          311          309          966          760          734 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
         506          401          305          300           NA          714 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
        2602         2379           NA         2371         1882         2068 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
        2935           NA         2963         2044         2687         2611 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
        2506         2481         2644         2212         2228         1810 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
        1910         1934         1507         1921         2022          512 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
         602          911          260           17          148          872 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
         728          686           53          135          669         1201 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A162 
         915          909           NA          112          892         1145 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
         991           20          478         1098         1135         1106 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
        1141         1119           80           NA           NA          910 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
         945         1023          324           21          568           43 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
         111          532          594          202          917          548 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
         206           48          213           30          926           39 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
         852          854          802          311           46           54 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
          NA          739           71          697           43          402 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
          22          555          513          548           63          458 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
          32           NA          107         1260           NA         1365 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BY TCGA-DI-A1C3 
           8          130          125          496         1114          739 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
        1076           NA           NA           NA         2797          711 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
        1471          519           NA          203          487          224 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
         511          332          243          328          972         1066 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH 
        1004          825          982          754          985           NA 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 
        1046          589         1069          392          826          820 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
         677          497           NA           NA          138          248 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL 
         741          826          710          710          693          425 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
         210          586          573          544          536          459 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
         490          378          481          260          197          588 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
         383          110          438          574          694          409 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
        1392          944          885          832          421          196 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX 
         545           65          212          113          161         1217 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
        1064         1034         1095           NA           NA          273 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 
        2941         1795          276           NA          881          761 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC 
         791           NA           53          400           74          329 
TCGA-QS-A5YQ TCGA-QS-A5YR 
         128          168 
Variable 1:'AGE':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=399,	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=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	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=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=27,	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"                                  
[6] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 488 columns, 1 survival variables, and 6 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=59, 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=5, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
