[1] "terrence_modification_tag"
[1] TRUE
[1] "dfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/miRseq_preprocessor/ESCA-TP/6154404/0.miRseq_preprocessor.Finished/ESCA-TP.miRseq_RPKM_log2.txt"
[1] "cfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ESCA-TP/6154407/ESCA-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/ESCA-TP/6154407/ESCA-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=22, in expression file=72, common to both=22
Number of genes in original expression dataset=517
[1] "ALL"
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"          "VITALSTATUS"           "DAYSTODEATH"          
 [4] "DAYSTOLASTFOLLOWUP"    "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
 [7] "PATHOLOGY.N.STAGE"     "PATHOLOGY.M.STAGE"     "DCCUPLOADDATE"        
[10] "GENDER"                "NUMBERPACKYEARSSMOKED" "GLEASON_SCORE"        
[13] "PSA_VALUE"             "DAYS_TO_PSA"           "BATCHNUMBER"          

Input Data has 15 rows and 22 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
          NA           NA           NA            1            8           16 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM 
          NA           NA           11          106          112          124 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU 
          NA          101           NA           NA          934          882 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
          NA           NA            4            2 
Variable 1:'AGE':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'NUMBERPACKYEARSSMOKED':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'PSA_VALUE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'DAYS_TO_PSA':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'BATCH.NUMBER':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
[4] "PATHOLOGY.N.STAGE"     "GENDER"                "NUMBERPACKYEARSSMOKED"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 22 columns, 1 survival variables, and 6 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=16, binary=FALSE, numeric=TRUE
HSA-MIR-27B 
        194 
NEOPLASM.DISEASESTAGE, nv=7, binary=FALSE, numeric=FALSE
HSA-MIR-148A 
          98 
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
HSA-MIR-580 
        438 
[1] "PATHOLOGY.T.STAGE"
[1] "num to class table"
vv1
1 2 3 4 
4 7 9 2 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
HSA-MIR-511-2 
          383 
[1] "PATHOLOGY.N.STAGE"
[1] "num to class table"
vv1
 0  1  2  3 
 8 10  3  1 
GENDER, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-628 
        457 
NUMBERPACKYEARSSMOKED, nv=12, binary=FALSE, numeric=TRUE
HSA-LET-7F-1 
           8 
[1] "saved param, results, example.expr in analysis.result.Rdata "
