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METABRIC data loading with MetaGxBreast #8

Closed recpe closed 2 years ago

recpe commented 2 years ago

Hi Dr. Haibe-Kains,

I'm using the package MetaGxBreast to extract gene expression data from METABRIC and TCGA. However, it seems the function was not working recently for MetaGxBreast (error message attached).

Would you please help to solve this issue?

Thank you!

library(MetaGxBreast) esets = MetaGxBreast::loadBreastEsets(loadString = c("TCGA","METABRIC"))[[1]] snapshotDate(): 2021-10-19 see ?MetaGxBreast and browseVignettes('MetaGxBreast') for documentation loading from cache see ?MetaGxBreast and browseVignettes('MetaGxBreast') for documentation loading from cache Error: failed to load resource name: EH1099 title: METABRIC reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded In addition: Warning message: file ‘4e9e48f5de98_1099’ has magic number 'SQLit' Use of save versions prior to 2 is deprecated

ChristopherEeles commented 2 years ago

Hi @recpe,

It looks like the file is corrupted in your ExperimentHub cache, and thus can't be loaded into R. You can fix this by deleting the offending files in your cache.

You can find the path of your cache using:

ExperimentHub::getExperimentHubOption("CACHE")

Then you will want to remove the file specified in the error message: 4e9e48f5de98_1099. If you don't have other files in your cache you could also just delete the whole folder, but this would get rid of any other datasets you have in the cache as well.

Best, Christopher Eeles Software Developer Haibe-Kains Lab PM-Research | UHN

ChristopherEeles commented 2 years ago

If this hasn't solved your problem please feel free to message here again.