
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/3471859/GBM-TP.medianexp.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/GBM-TP/3351055/GBM-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=574, in expression file=529, common to both=523
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 523 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-06-0140 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          238          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 
        1729          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         1561           60         1642 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
         578           77         1228         1126          801          866 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
         454          313          556          142          214           79 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
          12          196          166          151          360            6 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
         378          684           10          548          314          359 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
         455          313          168            8         2145          142 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
         245            5         1065          375           98          136 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
         293           62          717          285          678          594 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
         163           82           65           28          279          271 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
         204          218          699          178          165          637 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
         226          193          109          815          263          239 
TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
         413          127           33           23          149          282 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
          86          259          181          207          182          133 
TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
          13          285          341          107          254          138 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5417 TCGA-06-5418 
         268          273          260          204          155           83 
TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 
         114          186          138          236          163           44 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
         690         1057          119         3310           53          132 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
         419          316          231          103         1636           39 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
         195          458          685          447         1084          593 
TCGA-08-0359 TCGA-08-0360 TCGA-08-0373 TCGA-08-0375 TCGA-08-0380 TCGA-08-0385 
          29          352          134          279          330           31 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
         478           97          322            9           17          106 
TCGA-08-0511 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
         235          358          259          561         1770           39 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0522 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
         326          146          555          198          486          526 
TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
         168          438           49          316          181          218 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 
        2004            3          790          734           80          550 
TCGA-12-0707 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
          NA         1615         1311          167          277          451 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
         434         2790          753          562          323          715 
TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
         845         1179          271          626         3880          177 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
         189          929          658          364          346          482 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1597 TCGA-12-1598 
         277          442          121          103          427          287 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
         769          414          194         1807         1314          784 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
         351          333          358         1050          357          398 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
          98           61          459           29          188          701 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 
          68          342          418           99           41          164 
TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 
         502          801           62          879          485          587 
TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
          34          114          974          703          216           35 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
         917           28         1245          186          378           30 
TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
          59          540          542          232          179          217 
TCGA-14-2554 TCGA-14-2555 TCGA-14-3476 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 
         532          242           12          114          103          300 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
         581         1618          167          119          302          793 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
         496          130          882           25          301          406 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
         111          556          425          195          358          665 
TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
         262           13          434          103          327          276 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 
         181          394          141          772          106          217 
TCGA-19-1787 TCGA-19-1788 TCGA-19-1789 TCGA-19-1790 TCGA-19-1791 TCGA-19-2619 
         385          111           99          153            4          294 
TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 
         148           33          229            5          124          501 
TCGA-19-2631 TCGA-19-4068 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
         213          136          202          343          244          567 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
         242           54          198          164          161          165 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
         305          422          296          953          216          285 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
         286          452          167          269           37           48 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
         146          504           NA          555         1008          648 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
         914          427          350          752          316          316 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1745 
         489          231           87          438          479          344 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
           6           77          279          253          231          257 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-1760 TCGA-28-2502 
          36           46           86            4          143           20 
TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
         205          145          222          160          119          275 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
         473           77          298          432          237          415 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
         128          259          319          165          467          641 
TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
          15            3          482          593           36          142 
TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 
         386          451          515          372          632          456 
TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
         485          223          269          270          224          400 
TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
         338          112          383          356          330          165 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
          26          406          272          290           30          135 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-76-4925 TCGA-76-4926 TCGA-76-4927 
         183            6          351          145          138          535 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 TCGA-76-4934 TCGA-76-4935 
          94          111          278         1458           77          328 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-81-5910 
         507          100           82          519          253           49 
TCGA-87-5896 
           2 
Variable 1:'AGE':	nDistinctValues=72,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=327,	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=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=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=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
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] "HISTOLOGICAL.TYPE"                     
[5] "RADIATIONS.RADIATION.REGIMENINDICATION"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 523 columns, 1 survival variables, and 5 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
CLEC5A 
  1232 
AGE, nv=72, binary=FALSE, numeric=TRUE
FBXO17 
  5027 
GENDER, nv=2, binary=FALSE, numeric=FALSE
DDX3Y 
  939 
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
TM4SF20 
   9466 
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
CDH8 
 322 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
HOXD10 
  3964 
> q(save="no")
