
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/CESC-TP/2587666/0.mRNAseq_preprocessor.Finished/CESC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/CESC-TP/2587644/1.GDAC_clinicalDataPicker.Finished/CESC-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=40, in expression file=97, common to both=36
Number of genes in original expression dataset=18242
[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] "STOPPEDSMOKINGYEAR"                    
[13] "TOBACCOSMOKINGHISTORYINDICATOR"        
[14] "DISTANT.METASTASIS"                    
[15] "LYMPH.NODE.METASTASIS"                 
[16] "NUMBER.OF.LYMPH.NODES"                 
[17] "TUMOR.STAGECODE"                       
[18] "BATCHNUMBER"                           

Input Data has 18 rows and 36 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
        1505          925         5385           NA           NA         1616 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM 
          NA           NA           NA         2382         2155         1289 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OB TCGA-DS-A1OC 
          NA           81         2127         2892           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-EK-A2PI TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A23L 
          19           81           NA          178           37           37 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA 
          30           66            2           31           44          773 
Variable 1:'AGE':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
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=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
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:'STOPPEDSMOKINGYEAR':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'DISTANT.METASTASIS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'LYMPH.NODE.METASTASIS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'TUMOR.STAGECODE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "HISTOLOGICAL.TYPE"                     
 [3] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [4] "NUMBERPACKYEARSSMOKED"                 
 [5] "STOPPEDSMOKINGYEAR"                    
 [6] "TOBACCOSMOKINGHISTORYINDICATOR"        
 [7] "DISTANT.METASTASIS"                    
 [8] "LYMPH.NODE.METASTASIS"                 
 [9] "NUMBER.OF.LYMPH.NODES"                 
[10] "TUMOR.STAGECODE"                       
[1] "TUMOR.?STAGE" "10"          
[1] "stage2"
vv
 T1B T1B1 T1B2  T2A T2A1 T2A2  T2B  T3B 
   5   12    5    2    1    2    4    1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 36 columns, 1 survival variables, and 10 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
TBC1D10B|26000 
         15599 
AGE, nv=27, binary=FALSE, numeric=TRUE
ZNF660|285349 
        18049 
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
MST4|51765 
     10256 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
CDH17|1015 
      3180 
NUMBERPACKYEARSSMOKED, nv=9, binary=FALSE, numeric=TRUE
CHIT1|1118 
      3417 
STOPPEDSMOKINGYEAR, nv=3, binary=FALSE, numeric=TRUE
A2LD1|87769 
         19 
[1] "STOPPEDSMOKINGYEAR"
[1] "num to class table"
vv1
1978 1995 2011 
   1    2    1 
TOBACCOSMOKINGHISTORYINDICATOR, nv=4, binary=FALSE, numeric=TRUE
PDE6A|5145 
     11679 
[1] "TOBACCOSMOKINGHISTORYINDICATOR"
[1] "num to class table"
vv1
 1  2  3  4 
16 10  1  6 
DISTANT.METASTASIS, nv=2, binary=FALSE, numeric=FALSE
DMRT1|1761 
      4609 
LYMPH.NODE.METASTASIS, nv=2, binary=FALSE, numeric=FALSE
ARPM1|84517 
        981 
NUMBER.OF.LYMPH.NODES, nv=5, binary=FALSE, numeric=TRUE
NKX2-8|26257 
       10857 
[1] "NUMBER.OF.LYMPH.NODES"
[1] "num to class table"
vv1
 0  1  2  4 16 
21  7  2  1  1 
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
[1] "Clinical variable TUMOR.STAGECODE has too few non-missing values, n=0"
> q(save="no")
