[1] "terrence_modification_tag"
[1] TRUE
[1] "dfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/LUSC-TP/6044648/LUSC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt"
[1] "cfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LUSC-TP/6154711/LUSC-TP.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/LUSC-TP/6154711/LUSC-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=408, in expression file=482, common to both=398
Number of genes in original expression dataset=18519
[1] "ALL"
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [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] "GLEASON_SCORE"                         
[22] "PSA_VALUE"                             
[23] "DAYS_TO_PSA"                           
[24] "BATCHNUMBER"                           

Input Data has 24 rows and 398 columns.

[1] "Batch" "24"   
[1] "Last Follow UP"
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2466         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
         345          396         1810          862          758           49 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
        1331          187           85         2753           92          826 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
        3636         1426         3016         2133         1852         1058 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
         473          964         3724          283         3644          267 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
         962           NA         1268         1032          329          979 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
         608          223          131         1953           53          429 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 
         822           NA          622         1067         1470          734 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
          17         1161         1057          399           NA          587 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
          NA          358          965         1974         1932          444 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
        1345           24         1651         2170           NA          357 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
         573          915         1912         1713          505           29 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 
        2524         3469         2979         1311         5286         3149 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 
        4299          428           NA          334           NA          821 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
          80         1874          999         1528         2062         1715 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
          NA          707          365          428          941          551 
TCGA-34-5929 TCGA-34-7107 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
          NA           NA          120           13           12          199 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
         246          227          238          207           12          103 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
        1454         2253         1360         2086           NA         2130 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
        1848           52          740           59          832         1107 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2578 
         474         1084         1086          544           NA          684 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
        1176          822         1006          349          549          376 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 
         757          310           NA           NA          212           48 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 
        2023          202          193           NA          353          296 
TCGA-43-A56V TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 
         154           NA           NA           NA           NA           NA 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-51-6867 
         324          422           12           12          911           NA 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 
         541           NA          922           NA           NA          880 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 
           3          555           62           31           30           13 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
          30           44           40           26            6           NA 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
           1           41          177           36           63           17 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY 
          16           34           30           NA           46           30 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 
          31            4           NA            8           NA           NA 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46K 
         378          911         2167           NA         1058           NA 
TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 
        1113          707          641          109           NA          311 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
          NA           NA         2820          660         2446         1505 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
        2023         1259          274         1731         1531         1075 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
        1475         1296           96          982          908         1092 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-5128 TCGA-63-5131 TCGA-63-6202 
         717          815          358           NA           NA           NA 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 
          NA           NA           NA           NA           NA         1311 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
          61          641           30           31           61           28 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
          30           30          638          761           30           61 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 
          31           61           61           NA          700          578 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
          NA           61          578           NA          121           NA 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
         759           59          790         1217          699           NA 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
         699           NA          913           NA         1645          122 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
        1492           83          202          211          244           95 
TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
          NA           NA           NA           NA           NA           NA 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
          NA         2736           NA           15         1285           NA 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 
          NA           NA           NA          479           NA           NA 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
        1641           NA         2522           NA           NA           NA 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 
          NA         3166           NA           NA          833           NA 
TCGA-77-8146 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
        2183          293           NA         1683         1092           10 
TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5GB TCGA-77-A5GH TCGA-79-5596 TCGA-85-6175 
          NA         3576           NA          713           NA           NA 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
          11           24           34           18           10           49 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
           1           NA           35           38           60           26 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
          60           16          510          428           36           13 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
          11           44           54           60           55           67 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
          54           61           20           22           20          444 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC 
         423           NA          474           14           NA           NA 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
          NA           NA           25           19           NA           NA 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 
          NA           NA           24           13          757          289 
TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7340 
          89          358          428          244          331           82 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 
         106          122          160           69           87           NA 
TCGA-94-7943 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
         356         1213         1343          188          210          273 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
         183          256           NA          413          223          308 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE 
         222           35          449           36           92         1722 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1547         1135 
Variable 1:'AGE':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=133,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=250,	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=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=8,	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=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=128,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	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=54,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'PSA_VALUE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 23:'DAYS_TO_PSA':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 24:'BATCH.NUMBER':	nDistinctValues=29,	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] "YEAROFTOBACCOSMOKINGONSET"             
[12] "COMPLETENESS.OF.RESECTION"             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 398 columns, 1 survival variables, and 12 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=45, binary=FALSE, numeric=TRUE
PRSS12|8492 
      12827 
NEOPLASM.DISEASESTAGE, nv=9, binary=FALSE, numeric=FALSE
CENPE|1062 
      3357 
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
SFTPC|6440 
     14438 
[1] "PATHOLOGY.T.STAGE"
[1] "num to class table"
vv1
  1   2   3   4 
 95 241  44  18 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
KPNA2|3838 
      8593 
[1] "PATHOLOGY.N.STAGE"
[1] "num to class table"
vv1
  0   1   2   3 
251 104  33   5 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
DEDD|9191 
     4498 
GENDER, nv=2, binary=FALSE, numeric=FALSE
XIST|7503 
    17672 
KARNOFSKY.PERFORMANCE.SCORE, nv=8, binary=FALSE, numeric=TRUE
PPIAL4G|644591 
         12553 
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
SNIP1|79753 
      15098 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
C16ORF81|283860 
           1869 
NUMBERPACKYEARSSMOKED, nv=93, binary=FALSE, numeric=TRUE
ZBTB45|84878 
       17789 
YEAROFTOBACCOSMOKINGONSET, nv=54, binary=FALSE, numeric=TRUE
DUS1L|64118 
       4905 
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RNF113B|140432 
         13629 
[1] "saved param, results, example.expr in analysis.result.Rdata "
