[1] "terrence_modification_tag"
[1] TRUE
[1] "dfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_RPPA_preprocess/BRCA-TP/5956294/BRCA-TP.rppa.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=408, common to both=408
Number of genes in original expression dataset=142
[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 408 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04N TCGA-A2-A04P 
        1437          426           NA          852         3188           NA 
TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04Y 
        1275         2246          670           NA         1948         1099 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0CT 
        1963           NA         2813         2694         2298         2288 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0CY TCGA-A2-A0CZ 
          NA         1929         1947         1728         1673         1615 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EO 
         643         1051         1027          875          767         2441 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
        2426         2262         1127         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-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
        1534          533          520           NA          569          624 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE 
         531          575          631          989          769          553 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK 
         469          665          658          441          565          587 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG 
         445          964           NA         1165         1074         1043 
TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D 
        1079          930         1139          373         1006          965 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A8-A06N TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06U 
         326          387           NA          396          546           NA 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 
          NA          791           31          517         1641          274 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
         608          576          426          304          334          273 
TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A081 TCGA-A8-A082 TCGA-A8-A083 
         242          304          853           NA          549           NA 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08G TCGA-A8-A08H 
         458         1124          396           30          606           NA 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08T TCGA-A8-A08X 
          NA           NA          942          942         2830         1034 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A094 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A 
        1217          580           NA         1276          304          304 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09G TCGA-A8-A09I TCGA-A8-A09K 
         365           31          942           NA         1006          911 
TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A09Z TCGA-A8-A0A4 
         457          273           30           NA           NA          396 
TCGA-A8-A0A7 TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ 
          30            7           19           89           52          243 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
         223          197            5            9            9           10 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FS 
         195          140          241          212          230          191 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ 
         183           10           11           10           10           10 
TCGA-AN-A0G0 TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XT 
          16           10          375            9           10           10 
TCGA-AN-A0XU TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O 
          10          170         2442         1455         2031           NA 
TCGA-AO-A03P TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 
        2576           NA          997          651          735         1140 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
         617          680         1612         1542         1547         2190 
TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL 
        2334          650          798         1172         1887         1683 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
        2184         3119         2850         2877         2923         2754 
TCGA-AO-A12B TCGA-AO-A12C TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
        2359         1993         1948         1742         1471         1265 
TCGA-AO-A12H TCGA-AQ-A04L TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
         862         3957         2521         1500           NA         1138 
TCGA-AR-A0TT TCGA-AR-A0TU TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
        1679          360          904          739         1972           NA 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
        1313         1988         2134           NA         2316         1684 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AO 
        2298         1881         1604         1558         1485         1324 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AT TCGA-AR-A1AU TCGA-AR-A1AV 
        1215         1309         1242           NA         1409         1295 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-B6-A0I2 TCGA-B6-A0I6 TCGA-B6-A0I8 
        1072         1103          614         4360           NA           NA 
TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IO 
          NA           NA           NA         5383           NA         3350 
TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
        4284         2082         5748           NA           NA         5261 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
        4928           NA           NA         2721         3991         4788 
TCGA-B6-A0WX TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AY 
          NA           NA         5671          746         1180          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-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BJ 
        1733         1572         1132          974          781          660 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
        1876         1085         1481          826         1632         1640 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 
        1386         1519          355         1492         1270         1338 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
        1464         1305         1393          713         1156          673 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
         423         1467          476           77         1170         1374 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 
         133          477          435          292         1362         1405 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H5 
          NA          745          943          743          923         1080 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HK TCGA-BH-A0HL 
         747          701         1247         1611          178           72 
TCGA-BH-A0HN TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
         516          414          392         1560          829         1544 
TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18H 
         170          759         1288          268           61           NA 
TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-C8-A12K 
          NA           NA           NA           NA           NA           NA 
TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q 
          NA           NA           NA           NA           NA           NA 
TCGA-C8-A12T TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y 
          NA           NA           NA           NA           NA           NA 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A133 TCGA-C8-A134 
          NA           NA           NA           NA           NA           NA 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 
          NA          117            7          362          635          403 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-E2-A107 
         425          431          410          643          584         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-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14V 
        1358         1246         1163         1009         1013         1041 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 
         973          971          870          518          773          825 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
         707          591          640          726          450          762 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
         710          693          525          629          657          553 
TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
         393          589          274          626          234          395 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
         595          519          428          456         2328         1631 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
        1613          911          983          866          501          520 
Variable 1:'AGE':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=301,	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=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=14,	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=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=6,	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=19,	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=12,	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 408 columns, 1 survival variables, and 9 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=60, binary=FALSE, numeric=TRUE
ESR1|ER-ALPHA 
           51 
NEOPLASM.DISEASESTAGE, nv=10, binary=FALSE, numeric=FALSE
BCL2L1|BCL-XL 
           25 
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
MAPK14|P38_PT180_Y182 
                  138 
[1] "PATHOLOGY.T.STAGE"
[1] "num to class table"
vv1
  1   2   3   4 
 93 246  50  18 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
EIF4E|EIF4E 
        131 
[1] "PATHOLOGY.N.STAGE"
[1] "num to class table"
vv1
  0   1   2   3 
192 132  52  25 
PATHOLOGY.M.STAGE, nv=4, binary=FALSE, numeric=FALSE
BCL2L1|BCL-XL 
           25 
GENDER, nv=2, binary=FALSE, numeric=FALSE
AKT1 AKT2 AKT3|AKT_PT308 
                      19 
HISTOLOGICAL.TYPE, nv=6, binary=FALSE, numeric=FALSE
CDH1|E-CADHERIN 
             47 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
MAPK14|P38_PT180_Y182 
                  138 
NUMBER.OF.LYMPH.NODES, nv=19, binary=FALSE, numeric=TRUE
KDR|VEGFR2 
       118 
[1] "saved param, results, example.expr in analysis.result.Rdata "
