[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/GDAC_MethylationPreprocess/UCEC-TP/11494295/UCEC-TP.meth.by_min_clin_corr.data.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/UCEC-TP/11541775/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/11541775/UCEC-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=514, in expression file=431, common to both=397
Number of genes in original expression dataset=20302
[1] "ALL"
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [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 397 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0GG TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0VO 
          33           NA         2656         1167         1120          364 
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-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A059 TCGA-AP-A05O 
          71           30           82            4          250          371 
TCGA-AP-A0LF TCGA-AP-A0LM TCGA-AP-A0LS TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
         103          825         1918         2180         1836         1700 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
         952           NA         1276         1495          204          940 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
         317          847          494          555         1026           17 
TCGA-AX-A06D TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 
          NA          833         1845         1065         1333         1220 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
         404          584          516          412          464          617 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
         378          610         2337         2207         1646         2053 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
         764         1107          337           NA           NA         2167 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
        1020         1861         2090         1016         1232          589 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
         801          540          831           NA           NA         1177 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
           7            3           10            4            6           NA 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
           1            4           NA            7           36          254 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JX TCGA-B5-A0K8 
         440            4         1312         1483         1360          543 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
         125          265         5651         3448         2687         2303 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
        1656         1396         1362         1337         1232         1120 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
         976         1019          832          509          595          593 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
         596          560          528          504         5835           NA 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
          NA          438          447          356           NA          465 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
         389         3536         2929         2397         1890         1007 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0MA TCGA-BG-A0MH 
         153         1249         1038         1063           NA         1930 
TCGA-BG-A0MK TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
          NA          742          811          497         1043         1601 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
        1607         1721          451          382          419          448 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
         426          470          470          434           55          291 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CA 
        1085          721          612          344          207         1064 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD 
         311          309          966          760          734          506 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0U5 TCGA-BS-A0U9 
         401          305          300           NA         2935         2044 
TCGA-BS-A0UA TCGA-BS-A0UL TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
        2687         2481         1810         1910         1934         1507 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
        1921         2022          512          602          911          260 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
          17          148          872          728          686           53 
TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
         135          669         1201          915          909           NA 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A162 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
         112          892         1145          991           20          478 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
        1098         1135         1106         1141         1119           80 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
          NA           NA          910          945         1023          324 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
          21          568           43          111          532          594 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
         202          917          548          206           48          213 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
          30          926           39          852          854          802 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
         311           46           54           NA          739           71 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
         697           43          402           22          555          513 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
         548           63          458           32           NA          107 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
        1260           NA         1365            8          130          125 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
         826          496         1195         1114          739         1076 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ 
          NA           NA           NA         2797          711         1471 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX 
         519           NA          203          740          487          224 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
         511          332          572         1147          972         1066 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH 
        1004          825         1752          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-A1GJ TCGA-EY-A1GK 
         741          826          710          710          727          693 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR 
         425          210          586          573          544          536 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
         459          490          378          481          260          197 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
         588          383          110          438          574          694 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
         409         1392          944          885          832          421 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
         196          545           65          212          113          161 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
         179         1217         1064         1034         1095           NA 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
          NA          273         2941         1795          276           NA 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
         881          761          791           NA         1369           53 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 
         400           74          329          277          729          393 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
         213          342          212          573         1215          128 
TCGA-QS-A5YR 
         168 
Variable 1:'AGE':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=324,	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=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=7,	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 397 columns, 1 survival variables, and 6 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=58, 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 "
