
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/THCA/1677199/0.mRNAseq_preprocessor.Finished/THCA.uncv2.mRNAseq_RSEM_normalized_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/THCA/1669739/1.GDAC_clinicalDataPicker.Finished/THCA.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=193, in expression file=158, common to both=116
Number of genes in original expression dataset=17948
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "HISTOLOGICALTYPE"                      
[10] "RADIATIONS.RADIATION.REGIMENINDICATION"
[11] "NEOADJUVANTTHERAPY"                    
[12] "BATCHNUMBER"                           

Input Data has 12 rows and 116 columns.

[1] "Batch" "12"   
[1] "Last Follow UP"
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZB 
         479          356          232          197          251          122 
TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZJ TCGA-BJ-A190 TCGA-BJ-A28R TCGA-BJ-A28V 
         183          237          152           13          148          155 
TCGA-CE-A13K TCGA-CE-A27D TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DJ-A13M 
          16            3          231          952          161          274 
TCGA-DJ-A13P TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        4199          758          393          362          454          243 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QL 
         334         3041          549          212          243          212 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PO TCGA-DJ-A2PP 
          30          273           31          181          242          152 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
         318           59          312          242          234          153 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
         267          256          284          280          287          301 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DO-A1JZ 
         291          315          378          330          304         1225 
TCGA-DO-A1K0 TCGA-E8-A242 TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CW 
          93           34          580          153          214          245 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22P 
         217          284         1421         1209          650          174 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
         344          183         1088           10          903          589 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
         450          375           75          135           15          621 
TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N4 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39L 
         579         1049           43            9          362           59 
TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
        2535         1309         1413           20          237           51 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
         177          127           74          168          752           39 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A3DW 
          72          137         2095            9         3424          751 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A233 TCGA-FE-A236 TCGA-FE-A237 
        1565         1442          374          751         2031         2292 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FY-A2QD TCGA-FY-A3BL TCGA-H2-A26U 
        1215           NA         1907           38           35          106 
TCGA-IM-A3EB TCGA-IM-A3ED 
        1070          939 
Variable 1:'AGE':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=103,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=TRUE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=2,	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=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'BATCH.NUMBER':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "HISTOLOGICAL.TYPE"                     
[4] "RADIATIONS.RADIATION.REGIMENINDICATION"
[5] "NEOADJUVANT.THERAPY"                   
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 116 columns, 1 survival variables, and 5 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
[1] "Survival variable Time to Death has too few event occurrence, nEvent=1"
AGE, nv=55, binary=FALSE, numeric=TRUE
KBTBD2|25948 
        7885 
GENDER, nv=2, binary=FALSE, numeric=FALSE
DDX3Y|8653 
      4334 
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
PDHA1|5160 
     11475 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
FLJ37543|285668 
           5908 
NEOADJUVANT.THERAPY, nv=2, binary=FALSE, numeric=FALSE
SH2D1B|117157 
        14004 
> q(save="no")
