
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.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/SKCM-WT/3155025/SKCM-WT.uncv2.mRNAseq_RSEM_normalized_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-WT/3215660/SKCM-WT.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=23, in expression file=33, common to both=21
Number of genes in original expression dataset=18110
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "DAYSTOSUBMITTEDSPECIMENDX"             
 [5] "VITALSTATUS"                           
 [6] "DCCUPLOADDATE"                         
 [7] "PRIMARYSITEOFDESEASE"                  
 [8] "GENDER"                                
 [9] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[10] "RADIATIONTHERAPY"                      
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "DISTANT.METASTASIS"                    
[13] "LYMPH.NODE.METASTASIS"                 
[14] "TUMOR.STAGECODE"                       
[15] "NEOPLASM.DISEASESTAGE"                 
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 21 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D9-A149 TCGA-DA-A1IA TCGA-EE-A17Z 
          NA         1390           NA           NA           NA           NA 
TCGA-EE-A29D TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2MR TCGA-ER-A19L TCGA-ER-A1A1 
          NA           NA           NA           NA           NA         2386 
TCGA-FS-A1Z4 TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZU TCGA-GN-A261 
          NA           NA           NA           NA           NA           NA 
TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
          NA           NA          447 
Variable 1:'AGE':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 6:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                     "PRIMARY.SITE.OF.DISEASE"
[3] "GENDER"                  "LYMPH.NODE.METASTASIS"  
[5] "TUMOR.STAGECODE"         "NEOPLASM.DISEASESTAGE"  
[1] "TUMOR.?STAGE" "5"           
[1] "stage2"
vv
 T1 T1A  T2 T2A T3A T3B  T4 T4A T4B  TX 
  2   1   2   1   2   2   1   1   5   2 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 21 columns, 1 survival variables, and 6 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
ZNF720|124411 
        17964 
AGE, nv=18, binary=FALSE, numeric=TRUE
TRIM54|57159 
       16379 
PRIMARY.SITE.OF.DISEASE, nv=3, binary=FALSE, numeric=FALSE
AMBP|259 
     559 
GENDER, nv=2, binary=FALSE, numeric=FALSE
RPS4Y1|6192 
      13574 
LYMPH.NODE.METASTASIS, nv=6, binary=FALSE, numeric=FALSE
C12ORF61|283416 
           1686 
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
[1] "Clinical variable TUMOR.STAGECODE has too few non-missing values, n=0"
NEOPLASM.DISEASESTAGE, nv=9, binary=FALSE, numeric=FALSE
ZNF484|83744 
       17779 
> q(save="no")
