
R version 2.10.1 (2009-12-14)
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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.14.3949/ClinicalAnalysisAllGenes.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ClinicalAnalysisAllGenes_new.14.3949/", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/CESC-TP/3527692/CESC-TP.meth.by_min_expr_corr.data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/CESC-TP/3349247/CESC-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=47, in expression file=134, common to both=45
Number of genes in original expression dataset=20200
[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] "NUMBERPACKYEARSSMOKED"                 
[12] "DISTANT.METASTASIS"                    
[13] "LYMPH.NODE.METASTASIS"                 
[14] "NUMBER.OF.LYMPH.NODES"                 
[15] "TUMOR.STAGECODE"                       
[16] "NEOPLASM.DISEASESTAGE"                 
[17] "BATCHNUMBER"                           

Input Data has 17 rows and 45 columns.

[1] "Batch" "17"   
[1] "Last Follow UP"
TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MK 
        5385           NA           NA         1616           NA           NA 
TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
          NA         2382         2155         1289           NA           81 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1O9 TCGA-DS-A1OA TCGA-DS-A1OB TCGA-DS-A1OC 
        2127         2892           NA           NA           NA          376 
TCGA-DS-A1OD TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        3096          183            8           53           40           25 
TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EA-A439 TCGA-EA-A43B TCGA-EK-A2PI TCGA-EX-A1H5 
          19           81           20           54           NA          178 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
         241          211           37           37           30           66 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ 
           2           31           44           48           24          106 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
         773           NA          168 
Variable 1:'AGE':	nDistinctValues=30,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=33,	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=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'NUMBERPACKYEARSSMOKED':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TUMOR.STAGECODE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NEOPLASM.DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'BATCH.NUMBER':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "RADIATIONS.RADIATION.REGIMENINDICATION"
[3] "NUMBERPACKYEARSSMOKED"                 
[4] "DISTANT.METASTASIS"                    
[5] "LYMPH.NODE.METASTASIS"                 
[6] "NUMBER.OF.LYMPH.NODES"                 
[7] "TUMOR.STAGECODE"                       
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
 T1B T1B1 T1B2  T2A T2A1 T2A2  T2B  T3B   T4 
   5   16    5    2    3    3    5    1    1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 45 columns, 1 survival variables, and 7 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
HIST2H2AB 
     7756 
AGE, nv=30, binary=FALSE, numeric=TRUE
VPS25 
19077 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
ANKRD5 
   713 
NUMBERPACKYEARSSMOKED, nv=9, binary=FALSE, numeric=TRUE
 NPFF 
11908 
DISTANT.METASTASIS, nv=2, binary=FALSE, numeric=FALSE
TXNRD1__1 
    18644 
LYMPH.NODE.METASTASIS, nv=2, binary=FALSE, numeric=FALSE
TMEM139 
  17824 
NUMBER.OF.LYMPH.NODES, nv=6, binary=FALSE, numeric=TRUE
 TPK1 
18199 
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
[1] "Clinical variable TUMOR.STAGECODE has too few non-missing values, n=0"
> q(save="no")
