[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/GDAC_mRNA_Preprocess_Median/LUSC-TP/9830270/LUSC-TP.medianexp.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=154, common to both=154
Number of genes in original expression dataset=17814
[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 154 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-21-1070 TCGA-21-1071 TCGA-21-1072 
        1331          187           85         3636         1426         3016 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
        2134         1852         1058          474          965         3724 
TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
         284         3644          267          608          223           NA 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 
         131         1953           53          429          822         1485 
TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
         623         1470          734           17         1161         1057 
TCGA-22-4604 TCGA-22-4607 TCGA-22-4613 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 
         399          587          358         2524         3469         2979 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4589 TCGA-34-2596 TCGA-34-2600 
        1311         5287         3149           NA           80         1874 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5240 TCGA-34-5241 
         958          881         1000          951          365          428 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
         120           13           12          200          247          227 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 
         238          207           12         1454         2253         2086 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
         740           59         1107          474         1084         1086 
TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-46-3765 
        1223          684         1176          822         1007           NA 
TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-51-4079 TCGA-51-4080 
          NA           NA           NA           NA           12           12 
TCGA-51-4081 TCGA-56-1622 TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2706 
         911          881          642          109          311         2820 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
         661         2447         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-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
          NA           NA         1311           61          641           30 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
          31           61           28           30           30          639 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
         762           30           61           31           61           61 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
          NA          700          578           NA           61          578 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
          NA          121           NA          759           60          790 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 
        1217          699           NA          699           NA          913 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
          NA         1645          122         1492 
Variable 1:'AGE':	nDistinctValues=35,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=63,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=119,	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=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=2,	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=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=98,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=37,	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=8,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                         "NEOPLASM.DISEASESTAGE"      
 [3] "PATHOLOGY.T.STAGE"           "PATHOLOGY.N.STAGE"          
 [5] "PATHOLOGY.M.STAGE"           "GENDER"                     
 [7] "KARNOFSKY.PERFORMANCE.SCORE" "HISTOLOGICAL.TYPE"          
 [9] "NUMBERPACKYEARSSMOKED"       "COMPLETENESS.OF.RESECTION"  
[11] "RACE"                        "ETHNICITY"                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 154 columns, 1 survival variables, and 12 non-survival variables.
                              D                 
            "D" "Time to Death"          "Year" 
AGE, nv=35, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=7, 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 
 30 100  12  12 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "PATHOLOGY.N.STAGE"
[1] "num to class table"
vv1
 0  1  2  3 
96 40 13  5 
PATHOLOGY.M.STAGE, nv=2, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=5, binary=FALSE, numeric=TRUE
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "num to class table"
vv1
  0  50  70  90 100 
 18   2   1   4   1 
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=55, 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 "
