
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/SKCM-All_Samples/3154888/SKCM-All_Samples.uncv2.mRNAseq_RSEM_normalized_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-All_Samples/3215655/SKCM-All_Samples.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=211, in expression file=282, common to both=198
Number of genes in original expression dataset=18094
[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 198 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
          NA           NA           NA         3004           NA           NA 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JK 
          NA           NA           NA           NA          939           NA 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV 
          NA         1390           NA           NA           NA          164 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
          NA           NA           NA           NA           NA          122 
TCGA-D9-A3Z3 TCGA-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
          87          118         1484           NA         1555           NA 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
        1192           NA           NA         1354         1116           NA 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
          NA          680           NA           NA          534          451 
TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A299 TCGA-EB-A3HV TCGA-EB-A3XB 
          16           13           41           NA           39           36 
TCGA-EB-A3XC TCGA-EB-A3XD TCGA-EB-A3XE TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A3Y7 
           9           NA           NA            4           16           NA 
TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EB-A430 TCGA-EE-A17X 
           8            3            6           12           NA           NA 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
          NA           NA           NA           NA           NA         1097 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
         156           NA           NA         1155           NA         1175 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
         134           NA          825           NA          366          247 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 
         269          304          197           NA           NA           NA 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
         769          727           NA          272           NA           NA 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
          NA           NA           NA           NA           NA           NA 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19O TCGA-ER-A1A1 TCGA-ER-A3PL TCGA-FR-A2OS 
          NA         1303           NA         2386           52           NA 
TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A3YO TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YX 
         307          181           NA         2195           NA           NA 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZN TCGA-FS-A1ZP 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC 
          NA           NA         1637           NA          328          195 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A2C7 TCGA-GN-A261 
           6           31            4           NA           NA           NA 
TCGA-GN-A262 TCGA-GN-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
         756           NA           NA         2577           NA           NA 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-HR-A2OG TCGA-HR-A2OH 
          NA           NA           NA          447           NA           NA 
Variable 1:'AGE':	nDistinctValues=66,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=50,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=54,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=86,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=27,	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=FALSE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "PRIMARY.SITE.OF.DISEASE"               
[3] "GENDER"                                
[4] "RADIATIONS.RADIATION.REGIMENINDICATION"
[5] "DISTANT.METASTASIS"                    
[6] "LYMPH.NODE.METASTASIS"                 
[7] "TUMOR.STAGECODE"                       
[8] "NEOPLASM.DISEASESTAGE"                 
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
 T0  T1 T1A T1B  T2 T2A T2B  T3 T3A T3B  T4 T4A T4B TIS  TX 
  6   4  14   3  18  17   6   4  23  14   6   7  47   1  12 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 198 columns, 1 survival variables, and 8 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
RAB8B|51762 
      12864 
AGE, nv=66, binary=FALSE, numeric=TRUE
ACOX2|8309 
       177 
PRIMARY.SITE.OF.DISEASE, nv=4, binary=FALSE, numeric=FALSE
KRT17|3872 
      8400 
GENDER, nv=2, binary=FALSE, numeric=FALSE
ZFY|7544 
   17491 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
KDM4C|23081 
       8069 
DISTANT.METASTASIS, nv=5, binary=FALSE, numeric=FALSE
CLDN6|9074 
      3505 
LYMPH.NODE.METASTASIS, nv=10, binary=FALSE, numeric=FALSE
IHH|3549 
    7569 
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
[1] "Clinical variable TUMOR.STAGECODE has too few non-missing values, n=0"
NEOPLASM.DISEASESTAGE, nv=13, binary=FALSE, numeric=FALSE
TNFSF11|8600 
       16136 
> q(save="no")
