[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/miRseq_preprocessor/LUAD-TP/11489612/LUAD-TP.miRseq_RPKM_log2.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LUAD-TP/11541582/LUAD-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/LUAD-TP/11541582/LUAD-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=483, in expression file=513, common to both=474
Number of genes in original expression dataset=531
[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] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "COMPLETENESS.OF.RESECTION"             
[21] "RACE"                                  
[22] "ETHNICITY"                             
[23] "BATCHNUMBER"                           

Input Data has 23 rows and 474 columns.

[1] "Batch" "23"   
[1] "Last Follow UP"
TCGA-05-4244 TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 
          NA         1523           NA          607          426         1369 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 
        1126           NA           NA           NA         1431           NA 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 
         578          610           NA           NA          455           NA 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
         912          365          913          669          791          791 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
         761          761          730           NA          457          151 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
         882          670           30           62           14          225 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
         182          264         2973         3674         1147         1492 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
         864         1073          354         1357          448           NA 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
         133         1324         1429          400         1367          741 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
        1280         1301           97          246         1130         1163 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
        1036          190          722         1013          863          383 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
         723          328          302          845          704          658 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
         705         1938           NA         1864           NA          444 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
         592          366          218          557           NA          882 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
         535          719          385           99          260          486 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
         466          287          337          351          415           76 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
        2318           NA           NA           NA         1081         1421 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
         428          999          268          896          157         1700 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
         445          369          890          522          354           NA 
TCGA-49-AARQ TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
        6443           NA         2174         2146          455          785 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
         944         1499          246          282          267         1091 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
        2370          653           NA           NA          567          883 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
         764          686           NA           NA           NA           NA 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8460 
          NA           NA         1015           NA          255          105 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
          NA           NA          424          280          701         1178 
TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
        1479         1375           87            2          993           24 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6978 
          NA         1239           NA           25         1475           NA 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
          NA           67           NA           NA         1826           NA 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
        1233         2151         1170           53           18           35 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
         121            6            4           95           40          705 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
          39           39           34           24           54           44 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
          19           16          197           21            3           31 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
           5           33          462          100            6          600 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8204 TCGA-55-8205 
          26            4           47           15           NA           33 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          46           66          674          216           44           23 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
          29           11            8           15          228            9 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
           3          146          202          536           15           48 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
          49           66          106           33           42           29 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
          48           NA            1           28            5           47 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
         162           NA         1216         1289           NA         2696 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
        1445           NA           NA           NA           NA         2067 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
        2199           NA           NA         1246          910         1728 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
         628         1189         1686         1126           NA         2676 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
          62         1305          864         1559          866           31 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 
         610          573          427          385           NA          174 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
         141          422          202          186          690          414 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
         165          230          184           70           89          382 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
         100           77          129          214           61            3 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 
        1600          711          912           40          164          621 
TCGA-73-7499 TCGA-73-A9RS TCGA-75-5122 TCGA-75-5125 TCGA-75-5126 TCGA-75-5146 
         519          305           NA           NA           NA           NA 
TCGA-75-5147 TCGA-75-6203 TCGA-75-6205 TCGA-75-6206 TCGA-75-6207 TCGA-75-6211 
          NA           NA           NA           NA           NA           NA 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7030 TCGA-75-7031 
          NA           NA           NA           NA           NA           NA 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
          NA           NA           NA           NA           NA         1093 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
          NA         1202          760           NA           NA           NA 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
          NA         1221          678          215           NA         6812 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
          NA           NA           NA           NA           NA           NA 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
         327          881           NA          994         6346           NA 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-80-5611 
        2360           NA           NA           NA           NA           NA 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
         824           NA           NA           11          630          422 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
          NA          591           NA          508          745           10 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
          NA           13           24          479          489          476 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
         482           16           NA           19           26           35 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
          45           34           18           15          455          405 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
          10           30           NA           14           39          323 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
          NA           60          310           79          417          372 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
         842          224           35          492          505          174 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
          36           44          218          297          127          186 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
          34            2           NA          568          377          477 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
         476          830           84          121          553          605 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
         964         1965         1932         1332          775          181 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
          NA           22          107          182           NA           87 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 
         147           15          148          115          197          271 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
         392          427          459           44          170          154 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
         114          287          282          238          578          435 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV 
         116            6          266           NA          312          111 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         102          827         1175           84           NA           NA 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
          NA           NA           NA           NA           NA           NA 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
          NA           NA           NA           NA           NA           NA 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
         142           NA           NA           NA         1490          121 
Variable 1:'AGE':	nDistinctValues=50,	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=288,	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=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=35,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=93,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'BATCH.NUMBER':	nDistinctValues=26,	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] "KARNOFSKY.PERFORMANCE.SCORE"           
 [8] "HISTOLOGICAL.TYPE"                     
 [9] "RADIATIONS.RADIATION.REGIMENINDICATION"
[10] "NUMBERPACKYEARSSMOKED"                 
[11] "COMPLETENESS.OF.RESECTION"             
[12] "RACE"                                  
[13] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 474 columns, 1 survival variables, and 13 non-survival variables.
                              D                 
            "D" "Time to Death"          "Year" 
AGE, nv=50, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=8, 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 
146 264  43  18 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "PATHOLOGY.N.STAGE"
[1] "num to class table"
vv1
  0   1   2   3 
299  90  72   2 
PATHOLOGY.M.STAGE, nv=5, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=12, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=93, binary=FALSE, numeric=TRUE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
