[1] "terrence_modification_tag"
[1] TRUE
[1] "dfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/miRseq_preprocessor/BRCA-TP/6154457/0.miRseq_preprocessor.Finished/BRCA-TP.miRseq_RPKM_log2.txt"
[1] "cfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BRCA-TP/6154467/BRCA-TP.merged_data.txt"
[1] "gv"
[1] "ALL"
[1] "gfn"
[1] "ALL"
[1] "sfn"
[1] ""
[1] "fv"
[1] "ALL"
[1] "ofn"
[1] ""
[1] "dx"
[1] ""
[1] "sfn"
[1] ""
[1] FALSE
[1] "cfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BRCA-TP/6154467/BRCA-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=975, in expression file=995, common to both=954
Number of genes in original expression dataset=497
[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] "NUMBER.OF.LYMPH.NODES"                 
[18] "GLEASON_SCORE"                         
[19] "PSA_VALUE"                             
[20] "DAYS_TO_PSA"                           
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 954 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
         259          437         1320         1463          433         1437 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
         634          426           NA          242         1196          852 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
         583          553         3188           NA         1275         2499 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
        2246          670           NA         1948         1686         1099 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
        3819         1963           NA         3408         2813         2694 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
        3283         2298         2288           NA         1929         1947 
TCGA-A2-A0CY TCGA-A2-A0CZ TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
        1673         1615          643         1051         1027          875 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ 
         767         3093         2717         2441         3273         2426 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
        2262         1127         1066         1043          968          904 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
         752          735         3017         1661           NA           NA 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
        1534         1347          533          520           NA          569 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD 
         624          531          575          631          989          769 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL 
         469          665          658          441          587          445 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ 
         964           NA          714          528         1119          683 
TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
         616          583          595          501         1595         3276 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
         496          523          552         2796          322          635 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
        1205           NA         2525           NA          428         1505 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
        1168         1064          972         1166          222          274 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD 
         268          271          365          205          104         1165 
TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA 
        1074         1043         1079          930         1139          373 
TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H 
        1006          965          326          387          348          899 
TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J 
         954          459          333          399          369          627 
TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF 
         679          345          322          313          343          408 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SC TCGA-A7-A4SD 
         446          364          454          418          446          168 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A8-A06N TCGA-A8-A06O 
         371          544          177          210           NA          396 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y 
         396           31          546         1249           NA          791 
TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07C 
          31          517         1641          274         1004          580 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
         608          576          576          426          365          517 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
         304          334          273          242          303          304 
TCGA-A8-A07Z TCGA-A8-A081 TCGA-A8-A082 TCGA-A8-A083 TCGA-A8-A084 TCGA-A8-A085 
         853           NA          549           NA          458         1124 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08G TCGA-A8-A08H TCGA-A8-A08I 
         396           30          702          606           NA          365 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T 
          NA           NA          942           30          580         2830 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A090 TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
        1034         1217           NA          580          487          545 
TCGA-A8-A094 TCGA-A8-A095 TCGA-A8-A096 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A 
          NA         1276           NA          365          304          304 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09G TCGA-A8-A09I 
         365           31          396          942           NA         1006 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
         911          457           31          761          273          578 
TCGA-A8-A09X TCGA-A8-A09Z TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
          NA           NA          365          578          396          640 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
          30          396          517         1157           29           72 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
         329           81           44         1172         1162         1233 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH 
        1685         1125         1180           NA         1542           31 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
          28           69           30           21          451          286 
TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A62Y TCGA-AN-A03X 
          34           51           46           39           55           10 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
          10            7           10           19           89           54 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
          52          243          223          197            5            9 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK 
           9           10          195          140          241          212 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
         230          218          191          183           10           11 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0G0 TCGA-AN-A0XL TCGA-AN-A0XN 
          10           10           10           16           10           10 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
         375            9           10           10           10           10 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O 
         162          170         2442         1455         2031           NA 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
        2091         1456           NA          886          997          651 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
         537          735         1140          617          680         1612 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
         655         1542         1547         2190         2334          650 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 
         798         1172         1887         1683         2184         3119 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
        3018         2850         2877         2923         2754         2359 
TCGA-AO-A12C TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
        1993         1948         1742         1471         1265          862 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT 
         448         2513         1882         2140           16          541 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
         754          819         3957           NA          475          402 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
          77          665         2521         1500           NA         1138 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U2 
        1679          904         1972           NA         1313           NA 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
        2316         1684         2298         1881         1604         1558 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
        1485         1903         1329         1324         1215         1309 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AT TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
          NA         1242           NA         1409         1295         1072 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
        1103          614         3333         1548         2221         1990 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
        2074         1997           26         2008         1745         1888 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
        1620         1623         1648         1550         1465         1574 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
        1707         1373         1236         1212         1058           NA 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
        3913           NA         1303          223         1217          519 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
         633          516          620         1664          487          622 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I6 TCGA-B6-A0I8 
          NA           NA         4360         4549           NA           NA 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
          NA         6718           NA           NA           NA           NA 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
          NA         5383           NA         3836           NA         3350 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
        3374         4284         6434         2082         5748         7125 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
          NA           NA         5261         4928           NA           NA 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
          NA         2721         3991         4788           NA         5739 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
          NA          546           NA           NA         3941           NA 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI 
          NA           NA           NA         1326         3088         2236 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
        4233         5176          746         1180          622          777 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B1 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
         867         1427         1148         1203         1191         1471 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B8 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
        1732         1733         1569         1572         1132          974 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
         554          781          756          660         1339         1876 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
        1085         1481          826         1632         1640         1386 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
        1519          355         1492         1270         1338         1464 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
        1305         1393          948          713         1156          673 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
         423         1467          525          476           98           77 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
        1170         1374         1442          495          133          477 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EE 
         435          292         1362         1405           NA          943 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
         743          923          328          461         1149         1080 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HF 
         747          701         1247         1611          806          727 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HL TCGA-BH-A0HN TCGA-BH-A0HO TCGA-BH-A0HP 
         619          178           72          516           76          414 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
        1121          392         1560          829         1544          170 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F 
         728          759         1288         1363          701          268 
TCGA-BH-A18G TCGA-BH-A18H TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
          61           NA          220           NA           NA           NA 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 
          NA           NA           NA           NA          209           22 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
          NA           NA           NA           NA          323          196 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12K TCGA-C8-A12L 
         612           30         3323          271           NA           NA 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12T 
          NA           NA           NA           NA           NA           NA 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z 
          NA           NA           NA           NA           NA           NA 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A133 TCGA-C8-A134 TCGA-C8-A135 
          NA           NA           NA           NA           NA           NA 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
         117            7           NA           NA          345            2 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO 
           5            7          317            6            2           NA 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
           9            7           11           13            4            6 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
           1            1            1          371           30            1 
TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
           7          362          635          403          626          425 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
         431          410          643          584          431          532 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF 
         502          569          480          552          575          366 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL 
         366          426          577          611          612          611 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
         620          639          371          405          447          171 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
         236           85          272          727          839          552 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
          81          522          463          448          664          441 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
         606          538          242          499          482          496 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ 
         193          395          460          385          502          465 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
         471          115          432          429          530          487 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
         409          396          439          287          498          409 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
         145           23          307          397          381          373 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A106 TCGA-E2-A107 
         441          184          223         1308         1807         1046 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
         837         1417         1229         1141         1219          865 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
         878         1434         1358         1246         1163         1174 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
        1009         1013         1318         1041          973          971 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
         870          518          773          825          707          591 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C 
         640          726          450          762          710          693 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
         525          629          657          553          393          529 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P 
         589          274          626          234          395          595 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 
         519          428          456         2328         1631         1613 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE 
         911          983          866          501          520         1165 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
        1138          997         1026         1025          864          688 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
         117          675          637          337         1648          834 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
        1205          597          748         1231           NA          574 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A1LS TCGA-E2-A2P5 
        3246         3121           NA         1309          470          514 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E9-A1N3 
         167          478          219          549          677           NA 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
         583          507          410          365          399          653 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI 
         383          419          609          656           NA          300 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 
         362          434           19           64          185           42 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
          84          644          607          632         1224           20 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
         658          199          646          625          424          627 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D 
          24          381          404          712          692           NA 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 
         392          310          733          519           20           25 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS 
         827           58           28          381           21          540 
TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
          23          560           19          478           NA            7 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1IW TCGA-EW-A1IX 
          12            8            7           NA          371         1208 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
         258          554          575          403          504          477 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
         875          789          694          911          908         1229 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
        1250         1210         1611          907          703          562 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD 
         915           NA          575          608          186          424 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS 
         320          439         1050          606         1673         1604 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
         787          672          647          532          309          322 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
         212         3348           NA         5909         1615         1628 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
        1309         1299         1286         1883         1896         2762 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
        2331         2352         1622         3361         1162          981 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW 
        2108         1640         1753          412          551          360 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
         352          252           20           91          109          210 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
         168          143          484           85           64          385 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW 
        1416          229         1356          841          733          797 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I 
         513          429          313          298          448          721 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
        1658         1031          945          553          220          134 
Variable 1:'AGE':	nDistinctValues=65,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=107,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=629,	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=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=26,	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=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 19:'PSA_VALUE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'DAYS_TO_PSA':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=41,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "NEOPLASM.DISEASESTAGE"                 
[3] "PATHOLOGY.T.STAGE"                     
[4] "PATHOLOGY.N.STAGE"                     
[5] "PATHOLOGY.M.STAGE"                     
[6] "GENDER"                                
[7] "HISTOLOGICAL.TYPE"                     
[8] "RADIATIONS.RADIATION.REGIMENINDICATION"
[9] "NUMBER.OF.LYMPH.NODES"                 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 954 columns, 1 survival variables, and 9 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=65, binary=FALSE, numeric=TRUE
HSA-MIR-424 
        334 
NEOPLASM.DISEASESTAGE, nv=13, binary=FALSE, numeric=FALSE
HSA-MIR-210 
        158 
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
HSA-MIR-758 
        467 
[1] "PATHOLOGY.T.STAGE"
[1] "num to class table"
vv1
  1   2   3   4 
253 550 112  36 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
HSA-MIR-10A 
         23 
[1] "PATHOLOGY.N.STAGE"
[1] "num to class table"
vv1
  0   1   2   3 
450 319 106  63 
PATHOLOGY.M.STAGE, nv=4, binary=FALSE, numeric=FALSE
HSA-MIR-16-1 
         109 
GENDER, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-934 
        486 
HISTOLOGICAL.TYPE, nv=7, binary=FALSE, numeric=FALSE
HSA-MIR-210 
        158 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-3605 
         262 
NUMBER.OF.LYMPH.NODES, nv=28, binary=FALSE, numeric=TRUE
HSA-MIR-10A 
         23 
[1] "saved param, results, example.expr in analysis.result.Rdata "
