
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/UCEC-TP/3353328/UCEC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/UCEC-TP/3353073/UCEC-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=849, in expression file=370, common to both=369
Number of genes in original expression dataset=18627
[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] "RADIATIONTHERAPY"                      
[11] "HISTOLOGICALTYPE"                      
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "DISTANT.METASTASIS"                    
[14] "LYMPH.NODE.METASTASIS"                 
[15] "COMPLETENESS.OF.RESECTION"             
[16] "TUMOR.STAGECODE"                       
[17] "NEOPLASM.DISEASESTAGE"                 
[18] "BATCHNUMBER"                           

Input Data has 18 rows and 369 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
          NA         4053         1079          790         2165           NA 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
         275           97         2717         2516         1671         1750 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
        1447         1448         1477         1087         1167          780 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
         495          485          385          924          369           40 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ 
         125          294          555          128          927          177 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-AJ-A23M TCGA-AJ-A23O 
         241          348          292          243           31           60 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
          12           49           61         2545           NA          181 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
          NA         2026          250         1198         1364          831 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
         639          239          371          260           NA         3443 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
        2906         2986          103         1921           NA         2602 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
         965         2141          825         1992           NA         1875 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
        1668         1185          385         1816         1650         1329 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
         952           NA         1184         1131          204          691 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
         317          523          267           17           NA          603 
TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
         902         2191         1413         1075         1398         2024 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
        1064         1639           NA         1554          833          913 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
        1479         1065          868         1148         1333         1219 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
        2004          404          584          515          412          464 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
         617          378          610         2337         2207         1645 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 
        2052          764         1107          337           NA         2167 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
        1020         1861         2090         1016         1232          489 
TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IO TCGA-B5-A0JS TCGA-B5-A0JT 
         660          831           NA         1176         1241         1312 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
        1483         1125         1360          821          689          679 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
         746          682          700          466          426          372 
TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
         542          124          265         5279         3076         2317 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
        2038         1291         1396         1117         1147         1034 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
        1120          702          650          271          231          339 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU 
         337          315          291          259         5690           NA 
TCGA-B5-A1MV TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-BG-A0LW 
         380          174           NA          465          389          194 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 
         252          237          316          742          480          241 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
         698          690          765           NA          827          896 
TCGA-BG-A0MH TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
        1341           NA         1021          761          553          240 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
         231          128          224          260          131          490 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
         868          907         1151          279          186          230 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 
         231          252          155          169          220           46 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BK-A0C9 TCGA-BK-A0CA 
          14           NA           16          177          289          371 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BK-A26L TCGA-BS-A0T9 
         188          211          239          202          233           NA 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
         714         2260         2002           NA         2034         1443 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
        1514         2204           NA         2606         1749         2540 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
        1843           27           36         2191          595          149 
TCGA-BS-A0V6 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
        1650         1507         1661         1207          512           69 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
         690            8           17          147          578          350 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
         377           53           43          480         1012          915 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A162 TCGA-D1-A163 
         909           NA          112          892          976          938 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
          20          478          913          905          744          908 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
         909           80           NA           NA          742          640 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X 
         864          221           21          238           43          111 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
         532          324          202          506          347          206 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
          19          212            1          160           39          454 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
         429          459          311           46           54           NA 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
         326           70          396           43          311           22 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
         399          396            8            2          377           32 
TCGA-D1-A1O8 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-DI-A0WH TCGA-DI-A1BY 
          NA         1260           NA         1365          405         1114 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
         943           NA           NA          711         1289          427 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R 
          NA           66           46          332          328          972 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EY-A1G7 TCGA-EY-A1G8 
        1066         1004          761           NA           NA           NA 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
         138          248          552          532          527          506 
TCGA-EY-A1GK TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
         503          209          340          344          284          300 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A214 
         259          257          260          339          109          252 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
         391          235         1217         1064         1034         1095 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
          NA           NA          273         2557         1795          276 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
         880          761          791 
Variable 1:'AGE':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=32,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=296,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
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=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'DISTANT.METASTASIS':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'LYMPH.NODE.METASTASIS':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'TUMOR.STAGECODE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'NEOPLASM.DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=17,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "HISTOLOGICAL.TYPE"                     
[3] "RADIATIONS.RADIATION.REGIMENINDICATION"
[4] "COMPLETENESS.OF.RESECTION"             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 369 columns, 1 survival variables, and 4 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
KCNK10|54207 
        8242 
AGE, nv=55, binary=FALSE, numeric=TRUE
DIO2|1734 
     4640 
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
L1CAM|3897 
      8718 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
C8ORF79|57604 
         2582 
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
DGCR6|8214 
      4577 
> q(save="no")
