[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/miRseq_preprocessor/PCPG-TP/9830624/PCPG-TP.miRseq_RPKM_log2.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PCPG-TP/10006138/PCPG-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/PCPG-TP/10006138/PCPG-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=61, in expression file=179, common to both=61
Number of genes in original expression dataset=524
[1] "ALL"
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "DCCUPLOADDATE"                         
 [6] "GENDER"                                
 [7] "RADIATIONTHERAPY"                      
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "RACE"                                  
[10] "ETHNICITY"                             
[11] "BATCHNUMBER"                           

Input Data has 11 rows and 61 columns.

[1] "Batch" "11"   
[1] "Last Follow UP"
TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
         883           69           29          179          240         1094 
TCGA-PR-A5PH TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
         852          773          211           55           22          766 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RT-A6Y9 TCGA-RT-A6YA 
          70          134           24           29         2957         1249 
TCGA-RT-A6YC TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 
         246          604           89          216         1013          724 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D 
          32           26           37          356          191         2214 
TCGA-RW-A7D0 TCGA-SP-A6QD TCGA-SP-A6QH TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
          54         3087         1857         2983          274         3013 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MR TCGA-SR-A6MS TCGA-SR-A6MT 
          43            3         1558         2020         2222         3247 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
        3362         3269           NA          456          345         1106 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7HA 
         132          765          242          317          770           36 
TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A815 
         218          195          137          188           24          182 
TCGA-XG-A823 
         210 
Variable 1:'AGE':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=TRUE.
Variable 3:'DAYSTODEATH':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'BATCH.NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"    "GENDER" "RACE"  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 61 columns, 0 survival variables, and 3 non-survival variables.
AGE, nv=39, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
