HelenaLC/muscat

mmDS() and logcounts

Closed this issue · 4 comments

Nayrouz109 commented

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

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

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

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

Nayrouz109 commented

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