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ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ClinicalAnalysisAllGenes_new.13.3873/ClinicalAnalysisAllGenes.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ClinicalAnalysisAllGenes_new.13.3873/", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/miRseq_preprocessor/KICH-TP/3471875/0.miRseq_preprocessor.Finished/KICH-TP.miRseq_RPKM_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/KICH-TP/3351134/KICH-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=25, in expression file=66, common to both=25
Number of genes in original expression dataset=469
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                     "DAYSTODEATH"                     
 [3] "DAYSTOLASTFOLLOWUP"               "VITALSTATUS"                     
 [5] "DCCUPLOADDATE"                    "PRIMARYSITEOFDESEASE"            
 [7] "GENDER"                           "DATEOFINITIALPATHOLOGICDIAGNOSIS"
 [9] "RADIATIONTHERAPY"                 "KARNOFSKYPERFORMANCESCORE"       
[11] "HISTOLOGICALTYPE"                 "NUMBERPACKYEARSSMOKED"           
[13] "YEAROFTOBACCOSMOKINGONSET"        "DISTANT.METASTASIS"              
[15] "LYMPH.NODE.METASTASIS"            "TUMOR.STAGECODE"                 
[17] "NEOPLASM.DISEASESTAGE"            "BATCHNUMBER"                     

Input Data has 18 rows and 25 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 
        3126           NA         4335          247         1552         3473 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
         714         2674          775          788         1983         2211 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8430 TCGA-KN-8431 
         107           17           NA         2063           NA          712 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
          76          341         1124         2727          636         2303 
TCGA-KO-8409 
        2445 
Variable 1:'AGE':	nDistinctValues=24,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'NUMBERPACKYEARSSMOKED':	nDistinctValues=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'DISTANT.METASTASIS':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'LYMPH.NODE.METASTASIS':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'TUMOR.STAGECODE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "GENDER"                "DISTANT.METASTASIS"   
[4] "LYMPH.NODE.METASTASIS" "TUMOR.STAGECODE"       "NEOPLASM.DISEASESTAGE"
[1] "TUMOR.?STAGE" "5"           
[1] "stage2"
vv
T1A T1B  T2 T2B T3A  T4 
  3   5   8   4   4   1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 25 columns, 1 survival variables, and 6 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
[1] "Survival variable Time to Death has too few event occurrence, nEvent=2"
AGE, nv=24, binary=FALSE, numeric=TRUE
HSA-MIR-1248 
          33 
GENDER, nv=2, binary=FALSE, numeric=FALSE
HSA-LET-7F-1 
           8 
DISTANT.METASTASIS, nv=3, binary=FALSE, numeric=FALSE
HSA-MIR-939 
        461 
LYMPH.NODE.METASTASIS, nv=3, binary=FALSE, numeric=FALSE
HSA-MIR-1537 
         100 
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
[1] "Clinical variable TUMOR.STAGECODE has too few non-missing values, n=0"
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
HSA-MIR-1537 
         100 
> q(save="no")
