
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/READ-TP/3353353/READ-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/READ-TP/3352996/READ-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=336, in expression file=51, common to both=51
Number of genes in original expression dataset=18106
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "HISTOLOGICALTYPE"                      
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "DISTANT.METASTASIS"                    
[13] "LYMPH.NODE.METASTASIS"                 
[14] "COMPLETENESS.OF.RESECTION"             
[15] "NUMBER.OF.LYMPH.NODES"                 
[16] "TUMOR.STAGECODE"                       
[17] "NEOPLASM.DISEASESTAGE"                 
[18] "BATCHNUMBER"                           

Input Data has 18 rows and 51 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
         594          358          581          536          441          257 
TCGA-AF-6136 TCGA-AG-3591 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-4022 TCGA-AH-6549 
         231           NA           NA           30           30            6 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
          21           22          140          285          143         1825 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
         243          304          153          273          212          849 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
         212          608          121          152            8         3635 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6883 TCGA-EI-6884 
        3683          734          991           15          121           83 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 
         159          237           84           62           26           66 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
          12           31           20           21           16           33 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
          23           14         1451 
Variable 1:'AGE':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=TRUE.
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=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'COMPLETENESS.OF.RESECTION':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'TUMOR.STAGECODE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NEOPLASM.DISEASESTAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "RADIATIONS.RADIATION.REGIMENINDICATION"
[4] "DISTANT.METASTASIS"                    
[5] "LYMPH.NODE.METASTASIS"                 
[6] "COMPLETENESS.OF.RESECTION"             
[7] "NUMBER.OF.LYMPH.NODES"                 
[8] "TUMOR.STAGECODE"                       
[9] "NEOPLASM.DISEASESTAGE"                 
[1] "TUMOR.?STAGE" "8"           
[1] "stage2"
vv
 T1  T2  T3 T4A 
  3  10  31   7 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 51 columns, 1 survival variables, and 9 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
[1] "Survival variable Time to Death has too few event occurrence, nEvent=2"
AGE, nv=31, binary=FALSE, numeric=TRUE
PRR11|55771 
      12483 
GENDER, nv=2, binary=FALSE, numeric=FALSE
DDX3Y|8653 
      4362 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
GUSBL2|375513 
         6892 
DISTANT.METASTASIS, nv=4, binary=FALSE, numeric=FALSE
LHFPL5|222662 
         8636 
LYMPH.NODE.METASTASIS, nv=7, binary=FALSE, numeric=FALSE
HSPA5|3309 
      7416 
COMPLETENESS.OF.RESECTION, nv=3, binary=FALSE, numeric=FALSE
TEKT2|27285 
      15615 
NUMBER.OF.LYMPH.NODES, nv=14, binary=FALSE, numeric=TRUE
KCNF1|3754 
      7990 
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
[1] "Clinical variable TUMOR.STAGECODE has too few non-missing values, n=0"
NEOPLASM.DISEASESTAGE, nv=10, binary=FALSE, numeric=FALSE
METT11D1|64745 
          9745 
> q(save="no")
