Accessing legacy data in GDC

Question

[fr]

I am trying to retrieve legacy data from GDC through TCGAbiolinks. Specifically, I'd like to retrieve all RNAseq data for "CCLE-BLCA', which you can access through this link.

I ran

query <- GDCquery(project = "CCLE-BLCA", legacy = TRUE)

and got the full table with all project ids, name, etc. But I always get the error

Error in checkProjectInput(project) : Please set a valid project argument from the column project_id above. Project CCLE-BLCA was not found.

Are you aware of a way to download this data?

Answer 1

[Kevin Blighe]

Yes, on the GDC Legacy website, after you have filtered the project and samples that you want, download the file manifest and then use the GDC Data Transfer Tool, which will take the manifest as input, in order to download everything.