[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/mRNAseq_preprocessor/PRAD-TP/11493681/PRAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PRAD-TP/11541653/PRAD-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/PRAD-TP/11541653/PRAD-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=368, in expression file=486, common to both=360
Number of genes in original expression dataset=18276
[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] "RADIATIONTHERAPY"                      
[14] "HISTOLOGICALTYPE"                      
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "COMPLETENESS.OF.RESECTION"             
[17] "NUMBER.OF.LYMPH.NODES"                 
[18] "GLEASON_SCORE_COMBINED"                
[19] "GLEASON_SCORE_PRIMARY"                 
[20] "GLEASON_SCORE_SECONDARY"               
[21] "HIGHEST_GLEASON_SCORE"                 
[22] "GLEASON_SCORE"                         
[23] "PSA_RESULT_PREOP"                      
[24] "DAYS_TO_PREOP_PSA"                     
[25] "PSA_VALUE"                             
[26] "DAYS_TO_PSA"                           
[27] "RACE"                                  
[28] "ETHNICITY"                             
[29] "BATCHNUMBER"                           

Input Data has 29 rows and 360 columns.

[1] "Batch" "29"   
[1] "Last Follow UP"
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
         621         1332          671         1033          112          771 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
          91          212          671           31          395          425 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
          60           91          731           31          396         1065 
TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 
         943           31           62           28         1339          365 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
          31          700           31          458          731           62 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
         396          486          821          304          974         1004 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
          91          882          826         1007          595          405 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
         906         1415         1365          800         1391          880 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
         922          827          727         1184         1464         1116 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
        1476         1172         1102         1832         1416         1454 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
        1590         1962         1578         2079         1310         1115 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
        1179         1209         1832         1273         1456          884 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
         822         1491         1860         2542          663          295 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
         289          285          510          233          533          175 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
         842          191            9          727         1167          787 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
         781          625          442          430          552          596 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
         526          114          701          606         1961         1946 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
         821           NA          314          162          129          532 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
         299           93          229          668          536          393 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 
         417          560          278           91          230          864 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
         469          409          273          524          494           54 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
        1266         2657         2465         2068         2028         2110 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
        1696          554         2089         1515         1404         1542 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
        1501         1434         1415         1443         1378         1198 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
        1363          101         1222         1215         1156         1226 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
         811          958         1155         1393          765          830 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
        1771         1726         1608         1543         1164         1185 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
         849          942         1075          857          994           NA 
TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
         757          643          185          941          112          601 
TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
          NA          162           89           61           72          440 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
         868           24          870           60           51           72 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
          89           52           22           64           81           53 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
          45           51           63          748          792           60 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
          34           98          928           45          543          747 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
          56          589          682           95          726           66 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
          69           59          546          679           48          483 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
          35          680           23           54           61           67 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
          49          167           71          106           44           38 
TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
         134         2391         2684         2522           NA          614 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
         374          662          518          488          503          491 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
         624          454          523          183          405          528 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
         279          279          310          206          316          437 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X 
         617          422          178          323         2859         1712 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
        1359         1879         3524          913         1659         4604 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
        2056         2753         1498         3447         2040         1770 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL 
         840         1063          692           83          804           NA 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A723 TCGA-M7-A724 
         158          209          302          400          763          483 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
         573           97         1247         3487         1436         2620 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
         362          249          269          776          394          183 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 
         472          481          917         1001          459         3253 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
         805         2576         2879           NA         2309         1690 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
        1853         2037          663         1486          655          542 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK 
         176         1131          119         1157         1461          275 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
          91          790          958          972          868          930 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ 
         889          824         1126         1206          775         1611 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
        1491         1173         1124         2183         1890         1842 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
         512         1384         1261         1373           NA         1441 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
        1395         1155          798         3247         2170         1910 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX 
         213          427         1259           NA          740         1518 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
         862           50          150           34          239          183 
Variable 1:'AGE':	nDistinctValues=35,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=316,	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=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'GLEASON_SCORE_COMBINED':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'GLEASON_SCORE_PRIMARY':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'GLEASON_SCORE_SECONDARY':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 21:'HIGHEST_GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'GLEASON_SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 23:'PSA_RESULT_PREOP':	nDistinctValues=174,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 24:'DAYS_TO_PREOP_PSA':	nDistinctValues=180,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 25:'PSA_VALUE':	nDistinctValues=81,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 26:'DAYS_TO_PSA':	nDistinctValues=283,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 27:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 28:'ETHNICITY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 29:'BATCH.NUMBER':	nDistinctValues=22,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                       "PATHOLOGY.T.STAGE"        
 [3] "PATHOLOGY.N.STAGE"         "HISTOLOGICAL.TYPE"        
 [5] "COMPLETENESS.OF.RESECTION" "NUMBER.OF.LYMPH.NODES"    
 [7] "GLEASON_SCORE_COMBINED"    "GLEASON_SCORE_PRIMARY"    
 [9] "GLEASON_SCORE_SECONDARY"   "GLEASON_SCORE"            
[11] "PSA_RESULT_PREOP"          "PSA_VALUE"                
[13] "RACE"                     
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "2"          
[1] "PATHOLOGY.N" "3"          
Output Data has 360 columns, 1 survival variables, and 13 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=35, binary=FALSE, numeric=TRUE
PATHOLOGY.T.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "PATHOLOGY.T.STAGE"
[1] "num to class table"
vv1
  2   3   4 
147 206   5 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=10, binary=FALSE, numeric=TRUE
GLEASON_SCORE_COMBINED, nv=6, binary=FALSE, numeric=TRUE
GLEASON_SCORE_PRIMARY, nv=5, binary=FALSE, numeric=TRUE
[1] "GLEASON_SCORE_PRIMARY"
[1] "num to class table"
vv1
  2   3   4   5 
  1 167 168  24 
GLEASON_SCORE_SECONDARY, nv=4, binary=FALSE, numeric=TRUE
[1] "GLEASON_SCORE_SECONDARY"
[1] "num to class table"
vv1
  3   4   5 
107 202  51 
GLEASON_SCORE, nv=5, binary=FALSE, numeric=TRUE
[1] "GLEASON_SCORE"
[1] "num to class table"
vv1
  6   7   8   9  10 
 31 200  48  78   3 
PSA_RESULT_PREOP, nv=174, binary=FALSE, numeric=TRUE
PSA_VALUE, nv=81, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
