[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_RPPA_preprocess/GBM-TP/11489490/GBM-TP.rppa.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=214, common to both=211
Number of genes in original expression dataset=171
[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 211 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
TCGA-02-0003 TCGA-02-0004 TCGA-02-0011 TCGA-02-0014 TCGA-02-0068 TCGA-02-0069 
         144          345          630         2512          804          873 
TCGA-02-0116 TCGA-02-2470 TCGA-02-2485 TCGA-06-0125 TCGA-06-0126 TCGA-06-0128 
        1489          393          470         1439            3          691 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0154 TCGA-06-0155 TCGA-06-0156 TCGA-06-0171 
         989          320          389          263          164          396 
TCGA-06-0189 TCGA-06-0238 TCGA-06-0644 TCGA-06-0650 TCGA-06-0875 TCGA-06-0876 
         454          359          375          717         1322         1405 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
         204          218          699          165          637          226 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
         193          109          815          240          414         1031 
TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 
          NA           33           23          150           86          932 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 
         181          207          182          133          958          342 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
         108          254          138          268          273          260 
TCGA-06-5416 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 
         204          155           83          114          187          139 
TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 
         120          237          164           45           15          224 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
         253          391          145           47          145          151 
TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        1057         3310           53          132          419          316 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
         231          104         1637           39          195          458 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0360 
         685          447         1084          594           29          352 
TCGA-08-0373 TCGA-08-0375 TCGA-08-0380 TCGA-08-0385 TCGA-08-0386 TCGA-08-0389 
         134          279          330           31          478           97 
TCGA-08-0390 TCGA-08-0392 TCGA-12-0691 TCGA-12-0692 TCGA-12-1597 TCGA-12-1598 
         322            9          186           80          427          287 
TCGA-12-1599 TCGA-12-3646 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
         769         1315          351          333          358         1050 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5301 TCGA-14-0813 TCGA-14-0862 TCGA-14-0871 
         357          399           62           41           88          880 
TCGA-14-1823 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-1460 
         543          581         1618          168          119          195 
TCGA-19-0957 TCGA-19-0962 TCGA-19-1386 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 
         666           13          276          141          772          106 
TCGA-19-1786 TCGA-19-1788 TCGA-19-1789 TCGA-19-1790 TCGA-19-1791 TCGA-19-2619 
         218          112           99          154            4          294 
TCGA-19-2620 TCGA-19-2625 TCGA-19-2631 TCGA-19-4068 TCGA-19-5947 TCGA-19-5950 
         148          124          213          137          202          343 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
         244          567          144          242           54          198 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-26-1440 TCGA-26-1442 TCGA-26-5132 
         164          161          165          296          953          286 
TCGA-26-5133 TCGA-26-5134 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 
         452          167          241           71          146          505 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1836 TCGA-27-2518 TCGA-27-2528 
          NA          555         1008          914          753          480 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1750 TCGA-28-1752 TCGA-28-1753 TCGA-28-1757 
           6           77          254          258           37            4 
TCGA-28-1760 TCGA-28-5208 TCGA-28-5214 TCGA-32-1970 TCGA-32-1976 TCGA-32-1978 
         143          474          432          468           15          482 
TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-4210 TCGA-32-4211 
         142          386          452          515          113          383 
TCGA-32-5222 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
         323          272          290           30          135          360 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
           6          351          236          105          636          132 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 
         436          250          228          138          535           94 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 
         111          279         1458          100           82          519 
TCGA-76-6285 TCGA-76-6656 TCGA-76-6657 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
         254          147          153          282          235          237 
TCGA-81-5910 
          49 
Variable 1:'AGE':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=147,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=191,	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=18,	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=TRUE.
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"                                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 211 columns, 1 survival variables, and 6 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=57, 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
[1] "saved param, results, example.expr in analysis.result.Rdata "
