[1] "terrence_modification_tag"
[1] TRUE
[1] "dfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/SKCM-TM/6044638/SKCM-TM.uncv2.mRNAseq_RSEM_normalized_log2.txt"
[1] "cfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/SKCM-TM/6154803/SKCM-TM.merged_data.txt"
[1] "gv"
[1] "ALL"
[1] "gfn"
[1] "ALL"
[1] "sfn"
[1] ""
[1] "fv"
[1] "ALL"
[1] "ofn"
[1] ""
[1] "dx"
[1] ""
[1] "sfn"
[1] ""
[1] FALSE
[1] "cfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/SKCM-TM/6154803/SKCM-TM.merged_data.txt"
[1] "ok3"

nSamples in clinical file=260, in expression file=283, common to both=258
Number of genes in original expression dataset=18086
[1] "ALL"
[1] "terrence_modification_tag"
[1] TRUE
[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] "GLEASON_SCORE"                         
[20] "PSA_VALUE"                             
[21] "DAYS_TO_PSA"                           
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 258 columns.

[1] "Batch" "22"   
[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-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
        1483           NA          951           NA         4748         1709 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C1 TCGA-D3-A3C3 TCGA-D3-A3C6 
        1547         1371         3516           NA           NA           NA 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
        1007         1038         5052         2644           NA           NA 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
          NA           NA         3151          819          653         4923 
TCGA-D3-A51F TCGA-D3-A51G TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
        1329           NA         1221         4012          559          305 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
        1572          458         3373         4140         4195         5052 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
         226         3808         4609         1663          111          194 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
         345           98         1487           NA         3564           NA 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
        5926           NA           NA         3265         1861           NA 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
          NA          713           NA          870           NA         6553 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
         477           28          309          543          108         1182 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
          NA           NA           NA         3335           NA         2399 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
          NA           NA           NA         2452         1455           NA 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
        1205           NA          979           NA         1349           NA 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
        1716         1136          440         1700        10523           NA 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        5217           NA           NA         2401          743           NA 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        1787         1446         1315         9567         4134         5536 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
         686         2717         1664         1673         2296         2766 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
        3101           NA          435         1691          595         2042 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
          NA         3931           NA           NA           NA           NA 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
          NA           NA           NA           NA           NA         4403 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
        6175           NA           NA         7562           NA         3150 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
        4150         1265         1620         3781         3733          786 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J5 
         112          813           NA          714           NA           NA 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
          NA           NA         3095         4504           NA           NA 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
          NA           NA           NA         2365           NA           NA 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
          NA           NA           NA         8180           NA           NA 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19O TCGA-ER-A19P TCGA-ER-A19Q 
          NA           NA         1340           NA           NA           NA 
TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG 
        1133         2433           NA           NA          497          951 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A3YO 
         975           NA         2443         1010         2448           NA 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
        5298          148           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-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
          NA           NA           NA           NA          378           NA 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
        1504         2369            6          699         1446           NA 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 
          73          301          220           NA         3664           NA 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
        2577           NA           NA           NA           NA         1204 
Variable 1:'AGE':	nDistinctValues=66,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=121,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=131,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=206,	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=106,	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=28,	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:'GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'PSA_VALUE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 21:'DAYS_TO_PSA':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=13,	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 258 columns, 2 survival variables, and 10 non-survival variables.
                                                                              S 
                                    "S" "Time from Specimen Diagnosis to Death" 
                                        
                                "Month" 
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=66, binary=FALSE, numeric=TRUE
ACOX2|8309 
       177 
PRIMARY.SITE.OF.DISEASE, nv=4, binary=FALSE, numeric=FALSE
TMEM156|80008 
        15908 
NEOPLASM.DISEASESTAGE, nv=14, binary=FALSE, numeric=FALSE
RAI14|26064 
      12907 
PATHOLOGY.T.STAGE, nv=5, binary=FALSE, numeric=TRUE
INHA|3623 
     7697 
[1] "PATHOLOGY.T.STAGE"
[1] "num to class table"
vv1
 0  1  2  3  4 
21 30 57 49 53 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
C12ORF62|84987 
          1683 
[1] "PATHOLOGY.N.STAGE"
[1] "num to class table"
vv1
  0   1   2   3 
134  47  31  31 
PATHOLOGY.M.STAGE, nv=5, binary=FALSE, numeric=FALSE
LRRC28|123355 
         9226 
MELANOMA.ULCERATION, nv=2, binary=FALSE, numeric=FALSE
CDKL2|8999 
      3191 
MELANOMA.PRIMARY.KNOWN, nv=2, binary=FALSE, numeric=FALSE
FBXW12|285231 
         5748 
BRESLOW.THICKNESS, nv=106, binary=FALSE, numeric=TRUE
GBP4|115361 
       6279 
GENDER, nv=2, binary=FALSE, numeric=FALSE
ZFY|7544 
   17483 
[1] "saved param, results, example.expr in analysis.result.Rdata "
