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BioinformaticsFMRP / TCGAbiolinks

TCGAbiolinks
http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html
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Error in "matchedMetExp" when legacy=FALSE #570

Closed manwarA closed 1 year ago

manwarA commented 1 year ago

Hi, R4.2.1, TCGAbiolinks = 2.25.3

matchedMetExp("TCGA-LUSC") # gives the following error:

ooo By data.type Error in GDCquery(project = project, data.category = "Transcriptome Profiling", : Please set a valid workflow.type argument from the list below: => STAR - Counts

while with the legacy =T, it executed normally: matchedMetExp("TCGA-LUSC", legacy = TRUE).

So, I think the default should be legacy TRUE (instead of FALSE), as the number of samples returned is correct.

Plus, the document says that it returns the samples, however, the code specifically refers to the "primary tumor". It should be mentioned in the documents that it returns the primary tumor not the entire samples from the mentioned project.

tiagochst commented 1 year ago

Thank you for reporting the bug. I fixed it on my last commit.