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HelenaLC / muscat

Multi-sample multi-group scRNA-seq analysis tools
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mmDS() and logcounts #110

Closed Nayrouz109 closed 1 year ago

Nayrouz109 commented 1 year ago

Hello,

I have a question regarding the use of the mmDS(method = "dream"). In the paper, you mention that the method dream was used to fit a MM model on log-normalized data. So does that mean when I run the mmDS(method=dream) it will generate logcounts or do I need to specify whether to operate on counts or logcounts ?

Thanks,

plger commented 1 year ago

This is handled internally, you don't need to worry about it. Specifically, mmDS will use the count assay in combination with the sizeFactors() of the object.

Nayrouz109 commented 1 year ago

Thank you. Just to clarify, do I need to run computeLibraryFactors(sce) first to make sure sizefactors are added to my sce object before I run mmDS?

plger commented 1 year ago

If sizeFactors are empty, they will automatically be computed within mmDS (using computeLibraryFactors()).

Nayrouz109 commented 1 year ago

Thank you so much for the clarification, I appreciate it!