
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/GDAC_RPPA_preprocess/THCA-HistologicalType_Follicular/3698947/THCA-HistologicalType_Follicular.rppa.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/THCA-HistologicalType_Follicular/3811744/THCA-HistologicalType_Follicular.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=99, in expression file=52, common to both=52
Number of genes in original expression dataset=175
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "RADIATIONTHERAPY"                      
[10] "HISTOLOGICALTYPE"                      
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "RADIATIONEXPOSURE"                     
[13] "DISTANT.METASTASIS"                    
[14] "EXTRATHYROIDAL.EXTENSION"              
[15] "LYMPH.NODE.METASTASIS"                 
[16] "COMPLETENESS.OF.RESECTION"             
[17] "NUMBER.OF.LYMPH.NODES"                 
[18] "TUMOR.STAGECODE"                       
[19] "NEOPLASM.DISEASESTAGE"                 
[20] "MULTIFOCALITY"                         
[21] "TUMOR.SIZE"                            
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 52 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-BJ-A0Z2 TCGA-BJ-A0ZG TCGA-DE-A2OL TCGA-DJ-A13M TCGA-DJ-A13R TCGA-DJ-A13S 
         554          230          182          274           92          265 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QG TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A2PP 
         454          243          212          212           30          152 
TCGA-DJ-A2Q2 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DO-A1JZ TCGA-E3-A3DZ TCGA-EL-A3CP 
         206          378          330         1670          367         4831 
TCGA-EL-A3GQ TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
         918          549          602          592         1649         1734 
TCGA-EM-A1YE TCGA-EM-A22J TCGA-EM-A22L TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
        1645          440          318          432          500          543 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR 
         401          715          183           90          374          415 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AL 
         399          674          535          531          576          430 
TCGA-EM-A3AP TCGA-EM-A3FL TCGA-EM-A3FN TCGA-EM-A3FP TCGA-ET-A2N4 TCGA-ET-A2N5 
         254          510          367          529           81         1771 
TCGA-ET-A39I TCGA-ET-A39T TCGA-ET-A3DV TCGA-FE-A22Z 
         418         1799         4026         1799 
Variable 1:'AGE':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTODEATH':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=49,	numeric=TRUE,	binary=FALSE,	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=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'RADIATIONEXPOSURE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'DISTANT.METASTASIS':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'EXTRATHYROIDAL.EXTENSION':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'LYMPH.NODE.METASTASIS':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'COMPLETENESS.OF.RESECTION':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'TUMOR.STAGECODE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NEOPLASM.DISEASESTAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'MULTIFOCALITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'TUMOR.SIZE':	nDistinctValues=29,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                       "GENDER"                   
 [3] "RADIATIONEXPOSURE"         "DISTANT.METASTASIS"       
 [5] "EXTRATHYROIDAL.EXTENSION"  "LYMPH.NODE.METASTASIS"    
 [7] "COMPLETENESS.OF.RESECTION" "NUMBER.OF.LYMPH.NODES"    
 [9] "TUMOR.STAGECODE"           "NEOPLASM.DISEASESTAGE"    
[11] "MULTIFOCALITY"             "TUMOR.SIZE"               
[1] "TUMOR.?STAGE" "9"           
[1] "stage2"
vv
 T1 T1A T1B  T2  T3 T4A  TX 
  3   1   9  22  15   1   1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 52 columns, 0 survival variables, and 12 non-survival variables.
AGE, nv=34, binary=FALSE, numeric=TRUE
IGFBP2|IGFBP2-R-V 
               75 
GENDER, nv=2, binary=FALSE, numeric=FALSE
RPS6|S6-R-C 
        120 
RADIATIONEXPOSURE, nv=2, binary=FALSE, numeric=FALSE
AKT1S1|PRAS40_PT246-R-V 
                    109 
DISTANT.METASTASIS, nv=3, binary=FALSE, numeric=FALSE
VASP|VASP-R-C 
          144 
EXTRATHYROIDAL.EXTENSION, nv=3, binary=FALSE, numeric=FALSE
WWTR1|TAZ_PS89-R-C 
               138 
LYMPH.NODE.METASTASIS, nv=5, binary=FALSE, numeric=FALSE
RPS6KA1|P90RSK_PT359_S363-R-C 
                          175 
COMPLETENESS.OF.RESECTION, nv=3, binary=FALSE, numeric=FALSE
ERBB3|HER3-R-V 
            71 
NUMBER.OF.LYMPH.NODES, nv=5, binary=FALSE, numeric=TRUE
RPS6KA1|P90RSK_PT359_S363-R-C 
                          175 
[1] "NUMBER.OF.LYMPH.NODES"
[1] "num to class table"
vv1
 0  1  4  5  6 
32  1  2  2  1 
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
[1] "Clinical variable TUMOR.STAGECODE has too few non-missing values, n=0"
NEOPLASM.DISEASESTAGE, nv=5, binary=FALSE, numeric=FALSE
RAF1|C-RAF_PS338-R-C 
                  30 
MULTIFOCALITY, nv=2, binary=FALSE, numeric=FALSE
MAPK1|ERK2-R-C 
            59 
TUMOR.SIZE, nv=29, binary=FALSE, numeric=TRUE
RAF1|C-RAF_PS338-R-C 
                  30 
> q(save="no")
