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davismcc / archive-scater

An archived version of the scater repository, see https://github.com/davismcc/scater for the active version.
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Number of dimensions error in calculateQCMetrics #121

Closed samvidav closed 7 years ago

samvidav commented 7 years ago

Hi,

I am trying to run quality control on a large dataset (9000 samples, 29000 genes), so I'm working with an SCESet that is about 13Mb in size. Whenever I run the calculateQCMetrics function, I get this error - Error in pct_exprs_by_cell_sorted[1:500, ] : incorrect number of dimensions The function works fine for the same data when I break it into smaller chunks, but is giving me this error when I try to run it on the entire set. Do you have any ideas as to what could be going wrong?

Thanks

LTLA commented 7 years ago

Are you sure you're using the latest version of scater? I don't think pct_exprs_by_cell_sorted exists any more.

samvidav commented 7 years ago

I think that might be it, I updated all my packages and it runs fine now.