
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ClinicalAnalysisAllGenes_new.13.3873/ClinicalAnalysisAllGenes.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ClinicalAnalysisAllGenes_new.13.3873/", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BRCA-TP/3351778/BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/BRCA-TP/3349242/BRCA-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=903, in expression file=914, common to both=877
Number of genes in original expression dataset=18279
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "RADIATIONTHERAPY"                      
[11] "HISTOLOGICALTYPE"                      
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "DISTANT.METASTASIS"                    
[14] "LYMPH.NODE.METASTASIS"                 
[15] "NUMBER.OF.LYMPH.NODES"                 
[16] "TUMOR.STAGECODE"                       
[17] "NEOPLASM.DISEASESTAGE"                 
[18] "BATCHNUMBER"                           

Input Data has 18 rows and 877 columns.

[1] "Batch" "18"   
[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         3153           NA         1275         2364 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
        1950          670           NA         1918         1349          763 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
        3819         1827           NA         3408         2495         2392 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX 
        2298         1917           NA         1870         1750         1303 
TCGA-A2-A0CY TCGA-A2-A0CZ TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
        1288         1338          643          786          761          736 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0ER 
         496         2757         2515         2181         2053         1902 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
        1001          807          733          545          770          549 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX 
         485         1643         1351           NA           NA         1288 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
        1154          337          322           NA          456          395 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE 
         321          344          397          643          550          252 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK 
         289          404          379          358          326          334 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX 
         268          661           NA          460          221          935 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
         409          380          371          372          132         1285 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
        2968          258          285          243         2511          113 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3XZ TCGA-A2-A3Y0 
         363          803          428         1168          972          858 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
         170          253          166          161          188          159 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G 
         373          140          267          287          196          208 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
         551          421          257          209           64          122 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
          67          181          151          148           76           75 
TCGA-A7-A3RF TCGA-A8-A06N TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R 
          54           NA          396          396           31          546 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
        1249           NA           NA          791           31          517 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07C TCGA-A8-A07E TCGA-A8-A07F 
        1641          274         1004          580          608          576 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
         576          426          365          517          304          334 
TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A081 TCGA-A8-A082 
         273          242          303          304           NA          549 
TCGA-A8-A083 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08B TCGA-A8-A08C 
          NA          458         1124          396          702          607 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08H TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L 
         549          606           NA          365           NA           NA 
TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X 
         942          942           30          580         2830         1034 
TCGA-A8-A08Z TCGA-A8-A090 TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A094 
        1217           NA          580          487          545           NA 
TCGA-A8-A095 TCGA-A8-A096 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
        1276           NA          365          304          304          365 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09G TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
          31          396           NA         1006          911          457 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
          31          761          273          578          457           30 
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           44 
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           35          286 
TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AN-A03X TCGA-AN-A03Y 
          34           51           46           39           10           10 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D 
           7           10           19           89           54           52 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT 
         243          223          197            5            9           10 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
         195          140          241          212          230          218 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY 
         191          183           10           11           10           10 
TCGA-AN-A0FZ TCGA-AN-A0G0 TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
          10           16           10           10          375            9 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
          10           10           10           10          162          170 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R 
        2442         1455         1645           NA         2576         1707 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 
        1187           NA          886          585          302          294 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
         735          775          260          277         1255          346 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
        1547         1813         1965          354          449         1172 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
        1512         1319         1826         3119         3018         2850 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12C TCGA-AO-A12D 
        2877         2923         2754         2359         1993         1948 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
        1742         1471         1265          862          448         2513 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
        1519         2140           16          541          439          159 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ 
        3359           NA          230          162         2392         1500 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TU TCGA-AR-A0TV TCGA-AR-A0TW 
          NA         1138         1679          360          904          739 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A0U3 
          15           NA         1313            8           NA         2263 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
        1627         2298         1881         1604         1558         1485 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS 
        1329         1324         1215         1309           NA         1242 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
        1409         1295         1072         1103          614         3333 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
        1548         2221         1990         2074         1997           26 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
        2008         1745         1888         1620         1623         1648 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
        1550         1465         1574         1707         1373         1236 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK 
        1212         1058           NA         3913           NA         1303 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
         223         1217          519          633          516          620 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I6 TCGA-B6-A0I8 TCGA-B6-A0I9 
          NA         3826         4549           NA           NA           NA 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH 
        6718           NA           NA           NA           NA           NA 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
        5383           NA         3836           NA         3350         3374 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
        3871         6434         2082         5748         6795           NA 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
          NA         5261         4928           NA           NA           NA 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
        2721         3991         4788           NA         5396           NA 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
         546           NA           NA         3941           NA         5671 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI 
          NA           NA           NA         1326         3088         1463 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
        3330         4840          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         1117 
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-A0EB 
         376          292         1362         1405           NA          745 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
         943          743          917          328          461         1149 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
        1080          747          701         1247          856          806 
TCGA-BH-A0HF TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HL TCGA-BH-A0HN TCGA-BH-A0HO 
         727          619          178           72          516           76 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
         414         1121          392         1560          829          867 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
         170          180          175          543          558          372 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18H TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
         268           61           NA          220           NA           NA 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 
         209           22           NA           NA           NA           NA 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-C8-A12K TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N 
         323          196           NA           NA           NA           NA 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12T TCGA-C8-A12U TCGA-C8-A12V 
          NA           NA           NA           NA           NA           NA 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 
          NA           NA           NA           NA           NA           NA 
TCGA-C8-A132 TCGA-C8-A133 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
          NA           NA           NA           NA           26            7 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK 
          NA           NA           NA            2            5            7 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W 
           2            6            2           NA            9            7 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
          11           13            4            6            1            1 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y 
           1          371           30            1            7          264 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
         210           27          113           61          172           49 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
         344            2          256          248           18           NA 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH 
         178          273           57           96          187          284 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
          21          274          109          265          238          217 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
         167          105          123          106          171          236 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
          85          272          380          274          201           81 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
         155          197          196          352          326          319 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
         218          242          177          168           50          193 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
         149          146          117           81          120          166 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
         115           72          124          182          227          209 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
         140          185          118          125          144          145 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-E2-A105 
          23           90          135           73           15         1163 
TCGA-E2-A106 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
        1555          763          124         1172          352          748 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P 
         853          418          360         1350         1172          487 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
         974          845          834          890          838          748 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 
         833          692          688          518          591          588 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
         586          325          553          481          450          515 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
         502          496          315          517          468          315 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
          42          411          463           34          331          234 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
         395          315          330          274          267         1964 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1BC TCGA-E2-A1BD 
        1271         1361          911          774          297          317 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
         983          956          755          658          850          725 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
         518           14          392          448          127         1312 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
         633         1015          388          463          972           NA 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A1LS 
         350         2875         2750           NA         1014          239 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
         326          167          217           NA           NA           NA 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NE 
          NA           NA           NA           NA           NA           NA 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
          NA           NA           NA           NA           NA           NA 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
          19           64           29           42           84           34 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH 
          21         1228           20           47           38           14 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
          48           16           24           NA           NA           NA 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
          NA           NA           NA           NA           NA           43 
TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
          20           25           12           21           28           10 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3X8 TCGA-EW-A1IW 
          21           13           23           19           23          252 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        1082          258          282          139          252          227 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
         595          522          463          562          593          941 
TCGA-EW-A1P0 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
        1121          987          501          365          312          635 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE 
          NA          267          608          186          174          106 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV 
         139          875          139         1120         1173          238 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 
         190          647          229          212          703           NA 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH 
        5909         1615         1628         1309         1299         1286 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
        1883         1896         2762         2331         2352         1622 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-LL-A440 
        2982          743          981         1717         1640           20 
TCGA-LL-A441 
          91 
Variable 1:'AGE':	nDistinctValues=64,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=93,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=542,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'DISTANT.METASTASIS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'LYMPH.NODE.METASTASIS':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'TUMOR.STAGECODE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NEOPLASM.DISEASESTAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=27,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "HISTOLOGICAL.TYPE"                     
[4] "RADIATIONS.RADIATION.REGIMENINDICATION"
[5] "DISTANT.METASTASIS"                    
[6] "LYMPH.NODE.METASTASIS"                 
[7] "NUMBER.OF.LYMPH.NODES"                 
[8] "TUMOR.STAGECODE"                       
[9] "NEOPLASM.DISEASESTAGE"                 
[1] "TUMOR.?STAGE" "8"           
[1] "stage2"
vv
 T1 T1A T1B T1C  T2 T2B  T3 T3A  T4 T4B T4D  TX 
 38   1  10 185 507   1  97   1   7  25   2   3 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 877 columns, 1 survival variables, and 9 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
DIP2B|57609 
       4553 
AGE, nv=64, binary=FALSE, numeric=TRUE
ESR1|2099 
     5302 
GENDER, nv=2, binary=FALSE, numeric=FALSE
NLGN4Y|22829 
       10890 
HISTOLOGICAL.TYPE, nv=6, binary=FALSE, numeric=FALSE
CDH1|999 
    3200 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
CFHR1|3078 
      3372 
DISTANT.METASTASIS, nv=4, binary=FALSE, numeric=FALSE
ID2B|84099 
      7569 
LYMPH.NODE.METASTASIS, nv=16, binary=FALSE, numeric=FALSE
PIK3CA|5290 
      11983 
NUMBER.OF.LYMPH.NODES, nv=28, binary=FALSE, numeric=TRUE
HMSD|284293 
       7320 
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
[1] "Clinical variable TUMOR.STAGECODE has too few non-missing values, n=0"
NEOPLASM.DISEASESTAGE, nv=13, binary=FALSE, numeric=FALSE
C20ORF43|51507 
          2148 
> q(save="no")
