
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/GDAC_mRNA_Preprocess_Median/GBM-TP/2900562/0.GDAC_mRNA_Preprocess_Median.Finished/GBM-TP.medianexp.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/GBM-TP/2843145/1.GDAC_clinicalDataPicker.Finished/GBM-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=565, in expression file=529, common to both=519
Number of genes in original expression dataset=12042
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "KARNOFSKYPERFORMANCESCORE"             
[10] "HISTOLOGICALTYPE"                      
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "BATCHNUMBER"                           

Input Data has 12 rows and 519 columns.

[1] "Batch" "12"   
[1] "Last Follow UP"
TCGA-02-0001 TCGA-02-0003 TCGA-02-0004 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
         278          144          345          705          322         1077 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
         630         2511          627         1699         2361          612 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
        1614         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          556          208          447 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 
          97          458          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          828         2729          691 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
           7         1560          268         1757          515          106 
TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 
         821         1977          355          537          704         2817 
TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 
        3040          476         1489          503          514          538 
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          300          234          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          281          492 
TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
         102          511          393          465          469          492 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
           8          123         1439            3          108          691 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
         988          320          570          428          701          674 
TCGA-06-0139 TCGA-06-0141 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
         327          280          357           71          611          508 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0156 
         298          238          359          389          263          164 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 
          97          166           78         1729          161          579 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
          95          396            7           67           83         1561 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
          60         1642          578           77         1228         1126 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
         801          866          454          313          556          142 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 
         214           79           12          196          166          151 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
         360            6          378          684           10          548 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
         314          359          455          313          168            8 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 
        2145          142          245            5         1065          375 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
          98          136          293           62          717          285 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
         678          594          163           82           65           28 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
         279          271          204          218          699          178 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
         165          637          226          193          109          815 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 
         263          239          413          127           33           23 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
         149          282           86          259          181          207 
TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 
         182          133           13          285          341          107 
TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 
         254          138          268          273          260          204 
TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6389 
         155           83          114          186          138          236 
TCGA-06-6390 TCGA-06-6391 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
         163           44          690         1057          119         3310 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
          53          132          419          316          231          103 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
        1636           39          195          458          685          447 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0360 TCGA-08-0373 TCGA-08-0375 
        1084          593           29          352          134          279 
TCGA-08-0380 TCGA-08-0385 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
         330           31          478           97          322            9 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0511 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
          17          106          235          358          259          561 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0522 TCGA-08-0524 
        1770           39          326          146          555          198 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
         486          526          168          438           49          316 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 
         181          218         2004            3          790          734 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
          80          550           NA         1615         1311          167 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
         277          451          434         2790          753          562 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 
         323          715          845         1179          271          626 
TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
        3880          177          189          929          658          364 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
         346          482          277          442          121          103 
TCGA-12-1597 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 
         427          287          769          414          194         1807 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
        1314          784          351          333          358         1050 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 
         357          398           98           61          459           29 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 
         188          701           68          342          418           99 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 
          41          164          502          801           62          879 
TCGA-14-1034 TCGA-14-1037 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1451 
         485          587           34          114          974          703 
TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
         216           35          917           28         1245          186 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 
         378           30           59          540          542          232 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3476 TCGA-14-3477 
         179          217          532          242           12          114 
TCGA-14-4157 TCGA-15-0742 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 
         103          300          581         1618          167          119 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
         302          793          496          130          882           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          665          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          217          385          111           99          153 
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          136          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 
         216          285          286          452          167          269 
TCGA-26-5136 TCGA-26-5139 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
          37           48          146          504           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          752 
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 
         479          344            6           77          279          253 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
         231          257           36           46           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          473           77          298          432 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
         237          415          128          259          319          165 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
         467          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          451          515          372 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 
         632          456          485          223          269          270 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
         224          400          338          112          383          356 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
         330          165           26          406          272          290 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-76-4925 
          30          135          183            6          351          145 
TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 
         138          535           94          111          278         1458 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 
          77          328          507          100           82          519 
TCGA-76-6285 TCGA-81-5910 TCGA-87-5896 
         253           49            2 
Variable 1:'AGE':	nDistinctValues=72,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=324,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=384,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=4,	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=23,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'BATCH.NUMBER':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "KARNOFSKY.PERFORMANCE.SCORE"           
[4] "RADIATIONS.RADIATION.REGIMENINDICATION"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 519 columns, 1 survival variables, and 4 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
CLEC5A 
  1232 
AGE, nv=72, binary=FALSE, numeric=TRUE
RANBP17 
   5556 
GENDER, nv=2, binary=FALSE, numeric=FALSE
DDX3Y 
  939 
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
PPP3R1 
  3924 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NPAT 
4790 
> q(save="no")
