
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/mRNAseq_preprocessor/GBM/2008380/0.mRNAseq_preprocessor.Finished/GBM.uncv2.mRNAseq_RSEM_normalized_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/GBM/1971853/1.GDAC_clinicalDataPicker.Finished/GBM.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=565, in expression file=161, common to both=159
Number of genes in original expression dataset=18203
[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] "NEOADJUVANTTHERAPY"                    
[13] "BATCHNUMBER"                           

Input Data has 13 rows and 159 columns.

[1] "Batch" "13"   
[1] "Last Follow UP"
TCGA-02-0047 TCGA-02-0055 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0125 
         447           76          465          469          492         1439 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0138 TCGA-06-0141 TCGA-06-0152 
         988          320          570          674          280          359 
TCGA-06-0156 TCGA-06-0157 TCGA-06-0158 TCGA-06-0168 TCGA-06-0171 TCGA-06-0174 
         164           97          166          579          396           67 
TCGA-06-0178 TCGA-06-0184 TCGA-06-0187 TCGA-06-0190 TCGA-06-0210 TCGA-06-0211 
        1642         1228          801          313          151          360 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
          10          548          359          375           98          136 
TCGA-06-0649 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
          62          285          678          594          163           82 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0878 TCGA-06-0882 TCGA-06-1804 TCGA-06-2557 
          65           28          218          165          413           33 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
          23          149          282           86          259          181 
TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 
         207          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-08-0386 
         155           83          114          186          138          478 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0821 TCGA-12-1597 TCGA-12-3650 
         438           49          316          323          427          333 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-14-0736 TCGA-14-0781 
        1050          357          398           98          459           29 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0817 TCGA-14-0871 TCGA-14-1034 
          68          342          418          164          879          485 
TCGA-14-1402 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-15-0742 
         974          542          232          217          532          300 
TCGA-16-0846 TCGA-16-1045 TCGA-19-0957 TCGA-19-1389 TCGA-19-1390 TCGA-19-1787 
         119          882          665          141          772          385 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-4065 
         294          148            5          124          501          214 
TCGA-19-5960 TCGA-26-1442 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
         165          953          286          452          167          269 
TCGA-26-5136 TCGA-26-5139 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 
          37           48          146          504           NA         1008 
TCGA-27-1835 TCGA-27-1837 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 
         648          427          316          316          489          231 
TCGA-27-2526 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2499 TCGA-28-2509 
          87          479           77           36           94          145 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
         222          160          119          275          473           77 
TCGA-28-5213 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5220 TCGA-32-1970 
         298          237          415          128          319          467 
TCGA-32-1980 TCGA-32-1982 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 
          36          142          485          223          269          270 
TCGA-32-2638 TCGA-32-4213 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-3915 
         224          356          165           26          406          183 
TCGA-41-4097 TCGA-41-5651 TCGA-76-4925 TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 
           6          351          145          138          535           94 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 
         111          278         1458 
Variable 1:'AGE':	nDistinctValues=51,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=96,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=141,	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=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'BATCH.NUMBER':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "KARNOFSKY.PERFORMANCE.SCORE"           
[4] "RADIATIONS.RADIATION.REGIMENINDICATION"
[5] "NEOADJUVANT.THERAPY"                   
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 159 columns, 1 survival variables, and 5 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
MS4A3|932 
    10180 
AGE, nv=51, binary=FALSE, numeric=TRUE
CBARA1|10367 
        2783 
GENDER, nv=2, binary=FALSE, numeric=FALSE
XIST|7503 
    17353 
KARNOFSKY.PERFORMANCE.SCORE, nv=6, binary=FALSE, numeric=TRUE
ZNF415|55786 
       17825 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
ZBTB33|10009 
       17459 
NEOADJUVANT.THERAPY, nv=2, binary=FALSE, numeric=FALSE
NAIP|4671 
    10455 
> q(save="no")
