Question: R: Inconsistency between data from TCGAbiolinks and GDC (does TCGAbiolinks retrieve Legacy data by default?)
gravatar for fr
4.1 years ago by
fr150 wrote:


I'm using R and TCGAbiolinks to retrieve data and clinical data from GDC. To do so I use the following:

  clinquery<-GDCquery(project = "TCGA-LIHC",data.category = "Clinical")
  GDCdownload(clinquery, = 30)
  prepatientout<-GDCprepare_clinic(clinquery, = "patient")

However, I am finding some iconsistencies between what I'm getting and what is in GDC. For instance, for subject with 'bcr_patient_barcode=TCGA-DD-AADB' I retrieve the following data from 'GDCquery'

    bcr_patient_barcode gender  race_list   vital_status    neoplasm_histologic_grade   stage_event_pathologic_stage
18  TCGA-DD-AADF    FEMALE  ASIAN   Dead    G4  Stage I

However, when you look at the subject's data in GDC (here) everything is in agreement, with exception for Grade, which is never reported.


Could this mean that 'neoplasm_histologic_grade' is not the tumor grade? Or that 'GDCquery' is retrieving some Legacy data?

EDIT: this was now crossposted at github

rna-seq R genome • 1.7k views
ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by fr150
gravatar for fr
4.1 years ago by
fr150 wrote:

An answer to this question was added at the GitHub of TCGAbiolinks. Full credit goes to tiagochst (who is also here in biostars but I can't tag him).

ADD COMMENTlink written 4.1 years ago by fr150
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