GDCprepare with duplicated samples error when querying TCGA-STAD mutation data

lhcg1989613 commented 2 years ago

Hello!

I tried to download mutation data for project TCGA-STAD, but it showed an error with duplicated elements and "cases" column was NULL. Code shows as below.

query <- GDCquery( project = "TCGA-STAD", data.category = "Simple Nucleotide Variation", access = "open", legacy = FALSE, data.type = "Masked Somatic Mutation", workflow.type = "Aliquot Ensemble Somatic Variant Merging and Masking" ) GDCdownload(query) maf <- GDCprepare(query)

The errors show as below.

cases	experimental_strategy	analysis_workflow_type
	WXS	Aliquot Ensemble Somatic Variant Merging and Masking
	WXS	Aliquot Ensemble Somatic Variant Merging and Masking
	WXS	Aliquot Ensemble Somatic Variant Merging and Masking
	WXS	Aliquot Ensemble Somatic Variant Merging and Masking

Error in GDCprepare(query) : There are samples duplicated. We will not be able to prepare it

Is there any way of resolving this? Thanks in advance!

tiagochst commented 2 years ago

@lhcg1989613 Which version of TCGAbiolinks do you have installed ? It is working on my side with the github version: https://rpubs.com/tiagochst/issue_526

lhcg1989613 commented 2 years ago

Version of TCGAbiolinks is ‘2.25.2’. It may be a network problem.

BioinformaticsFMRP / TCGAbiolinks

GDCprepare with duplicated samples error when querying TCGA-STAD mutation data #526