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edvanburen / twosigma

twosigma
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Adjusting for library size #4

Closed ewynn610 closed 2 years ago

ewynn610 commented 2 years ago

Hi Eric,

Thank you for developing this package. I am working on implementing it on some single cell data and have a quick question. Does your package include any mechanism to adjust for differences in library size between cells, for example, by including normalization factors as model offsets like they do in edgeR or DESeq2?

Thanks,

Elizabeth

edvanburen commented 2 years ago

Hello Elizabeth,

Thank you to you for using the package! The package does not have a default adjustment for library size, unfortunately. I think the two options that are in the same vein are to: (1) use a normalization approach that produces integer normalized counts, and input them into twosigma or (2) include as a covariate something like the CDR (From the MAST paper) which is a surrogate for batch effects and, as I understand it, library size.

Does this help?

Thanks, Eric

ewynn610 commented 2 years ago

Yes, that is helpful.

Thanks! Elizabeth