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Bioconductor / OrchestratingSingleCellAnalysis

Content for the OSCA Book.
http://bioconductor.org/books/devel/OSCA/
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aggregateAcrossCells after fastMNN #47

Open StevenVanLaere opened 3 years ago

StevenVanLaere commented 3 years ago

Hi,

when I run aggregateAcrossCell on a data set created using fastMNN from multiple batches, an error is returned. Curiously, the object returned by fastMNN does not contain the raw counts, which I believe is the root of the error. How can this be fixed? Could it be due to the fact that I am not running the latest version of R/BioConductor?

Steven

LTLA commented 3 years ago

Well, as I often say, I'm not psychic, so I don't know what the problem is if I don't see the error. But I can make a few guesses.

This is probably a bug. But it's hard to know whether it might have already been fixed if you're on an old version of BioC.

However, the second point is that it's probably not a good idea to run aggregateAcrossCells() on the output of fastMNN. As you have noticed, the output does not contain raw counts, and you really shouldn't be using the corrected values for any gene-based downstream analyses, as discussed in Section 13.8. It's a better idea to use the raw counts to do your aggregation, based on the clusters derived from the corrected values (or in fastMNN()'s case, the corrected PCs).