
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/miRseq_preprocessor/SKCM-TM/4429102/0.miRseq_preprocessor.Finished/SKCM-TM.miRseq_RPKM_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-TM/4402018/SKCM-TM.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=242, in expression file=260, common to both=236
Number of genes in original expression dataset=600
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "DAYSTOSUBMITTEDSPECIMENDX"             
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "NEOPLASM.DISEASESTAGE"                 
 [8] "PATHOLOGY.T.STAGE"                     
 [9] "PATHOLOGY.N.STAGE"                     
[10] "PATHOLOGY.M.STAGE"                     
[11] "MELANOMA.ULCERATION"                   
[12] "MELANOMA.PRIMARY.KNOWN"                
[13] "BRESLOW.THICKNESS"                     
[14] "DCCUPLOADDATE"                         
[15] "GENDER"                                
[16] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[17] "RADIATIONTHERAPY"                      
[18] "RADIATIONS.RADIATION.REGIMENINDICATION"
[19] "BATCHNUMBER"                           

Input Data has 19 rows and 236 columns.

[1] "Batch" "19"   
[1] "Last Follow UP"
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
          NA           NA         3408           NA           NA         3687 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
          NA           NA         2326         2512           NA           NA 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
          NA           NA         3514           NA         2126           NA 
TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        1483          951           NA         4748         1709         1547 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C1 TCGA-D3-A3C3 TCGA-D3-A3C6 TCGA-D3-A3C7 
        1371         3516           NA           NA           NA         1007 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
        1038         5052         2644           NA           NA           NA 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
          NA         3151          819          653         4923         1329 
TCGA-D3-A51G TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
          NA         1221         4012          559          305         1572 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
         458         3373         4140          226         3808         4609 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
        1663          111          194          345           98         1487 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
          NA         3564           NA         5926           NA           NA 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
        3265         1861           NA           NA          713           NA 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
         870           NA         6553          477           28          309 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
          NA         3335           NA         2399           NA           NA 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
          NA         1455           NA         1205           NA          979 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
          NA         1349           NA         1716         1136          440 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        1700        10523           NA         5217           NA           NA 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
        2401          743           NA         1787         1446         1315 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
        9567         4134         5536          686         2717         1664 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
        1673         2296         2766         3101           NA          435 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
        1691          595         2042           NA         3931           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         4403         6175           NA           NA 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
        7562           NA         3150         4150         1265         1620 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
        3781         3733          786          112          813           NA 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
         714           NA           NA           NA           NA           NA 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
          NA           NA         2365           NA           NA           NA 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
          NA         8180           NA           NA           NA           NA 
TCGA-ER-A19N TCGA-ER-A19O TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2NC 
        1340           NA           NA           NA         2433           NA 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL 
         497          951          975           NA         2443         1010 
TCGA-FR-A3YN TCGA-FR-A3YO TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
        2448           NA           NA           NA           NA           NA 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
          NA         1225           NA           NA           NA           NA 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
          NA         3080           NA           NA           NA         4525 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
        1617           NA         1505           NA           NA         2366 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 
          NA           NA           NA           NA         2369            6 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A261 
         699         1446           NA          301          220           NA 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
        3664           NA         2577           NA           NA           NA 
TCGA-GN-A26A TCGA-GN-A26D 
          NA         1204 
Variable 1:'AGE':	nDistinctValues=65,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=112,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=118,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=170,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'NEOPLASM.DISEASESTAGE':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.T.STAGE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.N.STAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'PATHOLOGY.M.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MELANOMA.ULCERATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MELANOMA.PRIMARY.KNOWN':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'BRESLOW.THICKNESS':	nDistinctValues=99,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 17:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 19:'BATCH.NUMBER':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                     "PRIMARY.SITE.OF.DISEASE"
 [3] "NEOPLASM.DISEASESTAGE"   "PATHOLOGY.T.STAGE"      
 [5] "PATHOLOGY.N.STAGE"       "PATHOLOGY.M.STAGE"      
 [7] "MELANOMA.ULCERATION"     "MELANOMA.PRIMARY.KNOWN" 
 [9] "BRESLOW.THICKNESS"       "GENDER"                 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 236 columns, 1 survival variables, and 10 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
HSA-MIR-607 
        526 
AGE, nv=65, binary=FALSE, numeric=TRUE
HSA-MIR-204 
        173 
PRIMARY.SITE.OF.DISEASE, nv=4, binary=FALSE, numeric=FALSE
HSA-MIR-194-1 
          155 
NEOPLASM.DISEASESTAGE, nv=14, binary=FALSE, numeric=FALSE
HSA-MIR-199A-1 
           163 
PATHOLOGY.T.STAGE, nv=5, binary=FALSE, numeric=TRUE
HSA-MIR-1537 
         119 
[1] "PATHOLOGY.T.STAGE"
[1] "num to class table"
vv1
 0  1  2  3  4 
14 27 54 44 47 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
HSA-MIR-29A 
        217 
[1] "PATHOLOGY.N.STAGE"
[1] "num to class table"
vv1
  0   1   2   3 
123  38  28  27 
PATHOLOGY.M.STAGE, nv=5, binary=FALSE, numeric=FALSE
HSA-MIR-3654 
         336 
MELANOMA.ULCERATION, nv=2, binary=FALSE, numeric=FALSE
HSA-LET-7E 
         7 
MELANOMA.PRIMARY.KNOWN, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-582 
        516 
BRESLOW.THICKNESS, nv=99, binary=FALSE, numeric=TRUE
HSA-MIR-1537 
         119 
GENDER, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-361 
        318 
> q(save="no")
