[1] "libdir: /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/ClinicalAnalysisAllGenes_new/broadinstitute.org/cancer.genome.analysis/00333/58/"
[1] "terrence_modification_tag: TRUE"
[1] "op: "
[1] "dfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/LUSC-TP/9830261/LUSC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LUSC-TP/10006043/LUSC-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/LUSC-TP/10006043/LUSC-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=422, in expression file=489, common to both=419
Number of genes in original expression dataset=18516
[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] "RACE"                                  
[22] "ETHNICITY"                             
[23] "BATCHNUMBER"                           

Input Data has 23 rows and 419 columns.

[1] "Batch" "23"   
[1] "Last Follow UP"
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         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           50 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
        1331          187           85         2754           92          827 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
        3636         1426         3016         2134         1852         1058 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
         474          965         3724          284         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-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
         608          223           NA          131         1953           53 
TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
         429          822         1485          623         1067         1470 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
         734           17         1161         1057          399           NA 
TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
         587           NA          358          965         1975         1933 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
         445         1346           24         1651         2170           NA 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
         357          573          916         1912         1713          506 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
          29         2524         3469         2979         1311         5287 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 
        3149         4299          428           NA           NA           NA 
TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
         822           80         1874         1000         1528         2062 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
        1715           NA          707          365          428          941 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-37-3783 
         552           NA           NA          166           NA          120 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
          13           12          200          247          227          238 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
         207           12          103         1454         2253         1361 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
        2086           NA         2130         1849           52          740 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
          59          833         1107          474         1084         1086 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 
         544           NA         1223          684         1176          822 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
        1007          349          849          376          757          310 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
          NA           NA          212          236         2023          407 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V 
         358           NA          353          296          432          366 
TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 
          NA           NA           NA           NA           NA          324 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-51-6867 TCGA-52-7622 
         423           12           12          911           NA          541 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
          NA          923           NA           NA          881            3 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
         555           62           26           30           13           30 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 
          44           40           26            6           NA            1 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
          41          178           55           36           63           17 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY 
          16           34           38            2           46           30 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 
          25            4            4            8           NA           NA 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J 
         378          911         2167           NA         1058         2589 
TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 
          NA         1723         1072          910          642          109 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
          NA          311           NA           NA         2820          661 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
        2447         1505         2024         1260          274         1731 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
        1531         1075         1475         1297           97          983 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-5128 
         908         1092          717          816          358           NA 
TCGA-63-5131 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
          NA           NA           NA           NA           NA           NA 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 
          NA         1311           61          641           30           31 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
          61           28           30           30          639          762 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
          30           61           31           61           61           NA 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
         700          578           NA           61          578           NA 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
         121           NA          759           60          790         1217 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
         699           NA          699           NA          913           NA 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
        1645          122         1492           83          202          211 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 
         244           96          121          104           NA           NA 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
          NA           NA           NA           NA           NA         2737 
TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
          NA           15         1286           NA           NA           NA 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
          NA          479           NA           NA         1641           NA 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
        2522           NA           NA           NA           NA         3166 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8146 TCGA-77-8148 
          NA           NA          833           NA         2183          293 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
          NA         1684         1092           10           NA         4026 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB 
        3576           NA           NA         1290         1280           NA 
TCGA-77-A5GF TCGA-77-A5GH TCGA-79-5596 TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
         839          713           NA           NA          364          395 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 
          34           18           10           49            1           NA 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
          35          911           60           26           60           16 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
         960          428          513           13           11           13 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 
          54           60           55           67           54           61 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
          61           22           21          445          424           NA 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC 
           3          475           15           NA           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-85-A5B5 TCGA-90-6837 
          NA           NA           24           13          111          758 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE 
         289           89          358          428          244          331 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 
         269           82          106          122          160           70 
TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 
          87           NA          356          430         1213         1344 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 
         189          211          273          183          256           NA 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 
         413          224          308          222           35          449 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
          36           83         1722         1548         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=137,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=268,	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=4,	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=120,	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=96,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=55,	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=27,	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 419 columns, 1 survival variables, and 13 non-survival variables.
                              D                 
            "D" "Time to Death"          "Year" 
AGE, nv=45, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=9, 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 
100 252  48  19 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "PATHOLOGY.N.STAGE"
[1] "num to class table"
vv1
  0   1   2   3 
262 111  35   5 
PATHOLOGY.M.STAGE, nv=4, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=8, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=96, 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 "
