[1] "libdir: /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/ClinicalAnalysisAllGenes_new/broadinstitute.org/cancer.genome.analysis/00333/60/"
[1] "terrence_modification_tag: TRUE"
[1] "op: "
[1] "dfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/STAD-TP/11493722/STAD-TP.mRNAseq_RPKM_log2.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/STAD-TP/11541908/STAD-TP.merged_data.txt"
[1] "gv: ALL"
[1] "gfn: "
[1] "sfn: "
[1] "fv: ALL"
[1] "ofn: "
[1] "dx: "
[1] "cfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/STAD-TP/11541908/STAD-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=397, in expression file=274, common to both=274
Number of genes in original expression dataset=23365
[1] "ALL"
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "RADIATIONTHERAPY"                      
[14] "HISTOLOGICALTYPE"                      
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "COMPLETENESS.OF.RESECTION"             
[17] "NUMBER.OF.LYMPH.NODES"                 
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 274 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
         171          356           NA           NA           NA           NA 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4292 TCGA-BR-4294 TCGA-BR-4357 TCGA-BR-4361 TCGA-BR-4362 TCGA-BR-4363 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4366 TCGA-BR-4367 TCGA-BR-4368 TCGA-BR-4369 TCGA-BR-4370 TCGA-BR-4371 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6454 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        1055          485           NA          399          308          416 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
         213         1190           25           19          997          421 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
         402          491           38          273          642          940 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
         949         1002          390          280          753          728 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
         469          852           21            5          564          378 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
          29           21          388          569          532           25 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
          40           21          373           15          625           22 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8362 
         394            8          496          225          593           11 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
          NA          675           90           29          418          131 
TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 
         427           11          583          450           21            8 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
         482          113          164           22          280          615 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
          34          389          481           65          409            6 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8679 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
          15          351           NA          481          500           18 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CR 
         477           19          382           20           92           NA 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
          28          408          411          392           24           NA 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
         431           16          390           20          589          411 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5798 
          14          628          621           35          415           86 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
          99          400          401            2           NA           12 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
           2            2            3            4            5            3 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
           3            4           NA            4            3          193 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
           4            4            4            2            3            3 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
           3           92          822          485           NA          243 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4442 TCGA-CG-4443 
         245         1645           NA           NA           NA          912 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
        1431          580           NA           NA           NA          577 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4475 TCGA-CG-4476 TCGA-CG-4477 
          NA          365           NA          699           NA          942 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
          NA           NA           31           31           NA          183 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5732 
          30         3196           NA           NA           NA         1674 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
          NA          376          385          582          625          573 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
         564          566          543          181          523          126 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
         463          486          389          321          344          375 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
         752          511          593          523            7          212 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
         643          636          434          500          180          461 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 
         419          449          237          494          200          440 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
          NA          647           12          594           92          678 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
         519           NA           NA          413           17          337 
TCGA-HF-7131 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-7136 TCGA-HU-8238 
          NA           NA           NA           NA           NA           46 
TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
         434          347          368          323           23          739 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
         170          374          360          736           99          785 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
         358          650          912          273          198          190 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
         310            8           64          394          589          538 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
         374          294          270          268          834          645 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
          NA          572           NA           77 
Variable 1:'AGE':	nDistinctValues=51,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=66,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=170,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'HISTOLOGICAL.TYPE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=18,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL.TYPE"                     
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "COMPLETENESS.OF.RESECTION"             
[10] "NUMBER.OF.LYMPH.NODES"                 
[11] "RACE"                                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 274 columns, 1 survival variables, and 11 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=51, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=11, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "PATHOLOGY.T.STAGE"
[1] "num to class table"
vv1
  1   2   3   4 
 13  70 107  75 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "PATHOLOGY.N.STAGE"
[1] "num to class table"
vv1
 0  1  2  3 
91 76 46 49 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=7, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=26, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
