[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_mRNA_Preprocess_Median/GBM-TP/11489491/GBM-TP.medianexp.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/GBM-TP/11541538/GBM-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/GBM-TP/11541538/GBM-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=587, in expression file=528, common to both=525
Number of genes in original expression dataset=12042
[1] "ALL"
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "DCCUPLOADDATE"                         
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "RADIATIONTHERAPY"                      
[10] "KARNOFSKYPERFORMANCESCORE"             
[11] "HISTOLOGICALTYPE"                      
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCHNUMBER"                           

Input Data has 15 rows and 525 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
TCGA-02-0001 TCGA-02-0003 TCGA-02-0004 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
         279          144          345          705          322         1077 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
         630         2512          627         1699         2362          612 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
        1615         1300          748          315         2755           86 
TCGA-02-0034 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
         430          326          320          557          209          448 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 
          98          459          383          199          604          254 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 
         291          183          600          804          873          762 
TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 
         167          310          634          829         2729          691 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
           7         1561          268         1757          516          106 
TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 
         822         1977          355          537          705         2818 
TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 
        3041          476         1489          503          515          539 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
         327          440          121          422          432          485 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
         372          301          235          323            5          484 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
         782          133          764          322          377          441 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0439 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 
         321         1433           20          345          282          493 
TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
         102          511          393          466          470          493 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
           8          123         1439            3          109          691 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
         989          320          570          428          702          674 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
         327           NA          280           NA          357           71 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0152 TCGA-06-0154 
         611          508          298          239          359          389 
TCGA-06-0155 TCGA-06-0156 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 
         263          164           97          166           NA           78 
TCGA-06-0164 TCGA-06-0166 TCGA-06-0167 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
        1730          161           NA          579           95          396 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
           7           67           83         2768           61         1642 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
         578           77         1228         2246          801          866 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
         454          313          557          142          214           79 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
          12          197          167          151          360            6 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
         378          684           11          548          315          359 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
          NA          455          314          168            8         2145 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
         143          245            5         1065          375           98 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
         136          294           62          717          286          679 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
         595          164           82           66           28         1322 
TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
        1405          204          218          699          178          165 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 
         637          226          193          109          815          263 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
         240          414         1031           33           23          150 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
         282           86          932          181          207          182 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
         133           13          958          342          108          254 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5417 
         138          268          273          260          204          155 
TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6389 TCGA-06-6390 
          83          114          187          139          237          164 
TCGA-06-6391 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
          45          690         1057          119         3310           53 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
         132          419          316          231          104         1637 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
          39          195          458          685          447         1084 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0360 TCGA-08-0373 TCGA-08-0375 TCGA-08-0380 
         594           29          352          134          279          330 
TCGA-08-0385 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
          31          478           97          322            9           17 
TCGA-08-0510 TCGA-08-0511 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
         107          235          358          259          561         1770 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0522 TCGA-08-0524 TCGA-08-0525 
          39          327          146          555          199          486 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
         527          168          439           50          316          181 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 
         218         2005            3          790          734           80 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
         551           NA         1615         1311          167          277 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
         452          434         2791          754          562          323 
TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
         715          845         1179          272          626         3881 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 
         177          190          929          658          364          346 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1597 
         482          277          442          121          104          427 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
         287          769          414          195         1807         1315 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
         784          351          333          358         1050          357 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 
         399           98           62          460           29          189 
TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 
         701           68          342          419           99           41 
TCGA-14-0817 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 
         164          502          801           62          880          485 
TCGA-14-1037 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1451 TCGA-14-1452 
         587           34          114          975          703          216 
TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
          35          918           28         1246          187          378 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 
          30           60          541          543          232          179 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3476 TCGA-14-3477 TCGA-14-4157 
         218          532          242           12          115          104 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 
         300           NA          581         1618          168          119 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
         302          793          496          131          883           25 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
         301          406          111          556          425          195 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
         358          666          262           13          434          103 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 
         327          276          181          394          141          772 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1788 TCGA-19-1789 TCGA-19-1790 
         106          218          385          112           99          154 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
           4          294          148           33          229            5 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 TCGA-19-5947 TCGA-19-5950 
         124          501          213          137          202          343 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
         244          567          242           54          198          164 
TCGA-19-5959 TCGA-19-5960 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
         161          165          305          422          296          953 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
         217          285          286          452          167          270 
TCGA-26-5136 TCGA-26-5139 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
          37           48          146          505           NA          555 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
        1008          648          914          427          350          753 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
         316          316          489          231           87          438 
TCGA-27-2528 TCGA-28-1745 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 
         480          345            6           77          280          254 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
         232          258           37           47           86            4 
TCGA-28-1760 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 
         143           20          205          145          222          160 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5213 TCGA-28-5214 
         119          275          474          442          951          432 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
         237          415          128          690          319          165 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
         468          641           15            3          482          593 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
          36          142          386          452          515          372 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 
         632          457          485          224          269          693 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
         644          643          604          113          383          604 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
         330          323           26          406          272          290 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-76-4925 
          30          135          360            6          351          146 
TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 
         138          535           94          111          279         1458 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 
          77          328          508          100           82          519 
TCGA-76-6285 TCGA-81-5910 TCGA-87-5896 
         254           49          800 
Variable 1:'AGE':	nDistinctValues=72,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=349,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=382,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'DCCUPLOADDAY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH.NUMBER':	nDistinctValues=17,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "KARNOFSKY.PERFORMANCE.SCORE"           
[4] "HISTOLOGICAL.TYPE"                     
[5] "RADIATIONS.RADIATION.REGIMENINDICATION"
[6] "RACE"                                  
[7] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 525 columns, 1 survival variables, and 7 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=72, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
