[1] "libdir: /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/ClinicalAnalysisAllGenes_new/broadinstitute.org/cancer.genome.analysis/00333/69/"
[1] "op: "
[1] "dfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/OV-TP/14527532/OV-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/OV-TP/15085780/OV-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/OV-TP/15085780/OV-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=590, in expression file=261, common to both=261
Number of genes in original expression dataset=18555
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                                    
 [2] "VITAL_STATUS"                                      
 [3] "DAYS_TO_DEATH"                                     
 [4] "DAYS_TO_LAST_FOLLOWUP"                             
 [5] "PRIMARY_SITE_OF_DISEASE"                           
 [6] "NEOPLASM_DISEASESTAGE"                             
 [7] "PATHOLOGY_T_STAGE"                                 
 [8] "PATHOLOGY_N_STAGE"                                 
 [9] "PATHOLOGY_M_STAGE"                                 
[10] "DCC_UPLOAD_DATE"                                   
[11] "GENDER"                                            
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"              
[13] "RADIATION_THERAPY"                                 
[14] "KARNOFSKY_PERFORMANCE_SCORE"                       
[15] "EXAMINATIONS_EXAMINATION_KARNOFSKYPERFORMANCESCORE"
[16] "HISTOLOGICAL_TYPE"                                 
[17] "TUMOR_GRADE"                                       
[18] "TUMOR_STAGE"                                       
[19] "PATIENT_TUMOR_RECURRENCE_STATUS"                   
[20] "DAYS_TO_TUMOR_RECURRENCE"                          
[21] "CHEMOTHERAPY"                                      
[22] "RADIATIONS_RADIATION_REGIMENINDICATION"            
[23] "COMPLETENESS_OF_RESECTION"                         
[24] "RACE"                                              
[25] "ETHNICITY"                                         
[26] "BATCH_NUMBER"                                      

Input Data has 26 rows and 261 columns.

[1] "Batch" "26"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=47,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=138,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=222,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE excluded in the analysis because there is no case of (both >= 3) in the table below"
              OMENTUM OVARY  
freq.values   "1"     "260"  
freq.contrast "260"   "1"    
both >= 3     "FALSE" "FALSE"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "NEOPLASM_DISEASESTAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_T_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_N_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'EXAMINATIONS_EXAMINATION_KARNOFSKYPERFORMANCESCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "EXAMINATIONS_EXAMINATION_KARNOFSKYPERFORMANCESCORE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'HISTOLOGICAL_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HISTOLOGICAL_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 17:'TUMOR_GRADE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_GRADE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 18:'TUMOR_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 19:'PATIENT_TUMOR_RECURRENCE_STATUS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATIENT_TUMOR_RECURRENCE_STATUS is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 20:'DAYS_TO_TUMOR_RECURRENCE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_TUMOR_RECURRENCE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 21:'CHEMOTHERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "CHEMOTHERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 22:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION excluded in the analysis because there is no case of (both >= 3) in the table below"
              NO      YES    
freq.values   "2"     "259"  
freq.contrast "259"   "2"    
both >= 3     "FALSE" "FALSE"
Variable 23:'COMPLETENESS_OF_RESECTION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "COMPLETENESS_OF_RESECTION excluded in the analysis because there is no case of (both >= 3) in the table below"
              R0      R1     
freq.values   "2"     "5"    
freq.contrast "5"     "2"    
both >= 3     "FALSE" "FALSE"
Variable 24:'RACE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 25:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 26:'BATCH_NUMBER':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 261 columns, 1 survival variables, and 4 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"              "KARNOFSKY_PERFORMANCE_SCORE"
[3] "RACE"                        "ETHNICITY"                  
[1] "DAYS_TO_DEATH_OR_LAST_FUP"
[1] "DAYS_TO_DEATH_OR_LAST_FUP"
[1] "D"                         "DAYS_TO_DEATH_OR_LAST_FUP"
[3] "Month"                    
[1] "check if there is any case_to_report in survival time data or not"
[1] "alarming case(s) exist!"
[1] "[  1  ] case_to_report(s) is(are) excluded in survival analysis"
YEARS_TO_BIRTH, nv=47, binary=FALSE, numeric=TRUE
KARNOFSKY_PERFORMANCE_SCORE, nv=3, binary=FALSE, numeric=TRUE
[1] "KARNOFSKY_PERFORMANCE_SCORE"
[1] "num to class table"
vv1
 60  80 100 
  5   8   1 
RACE, nv=5, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
