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Hello, I am using MAST to find DE through two different conditions (disease and health) in a single-nucleus transcriptomic data, and so far I have cells obtained from 3 sick subjects and 3 healthy subjects. The cells obtained from the 6 subjects were sequenciated all together therefore I have a single "batch". I am looking for DE in a single cell type and comparing between the two conditions, disease and health. How do I include the variable "donor identification" in the model? Should I add the donor id as a covariate? What happens when you have many donors, do I add each donor id as a covariate as well? Thank you very much for your help!

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sessionInfo( )

You can't model both donor and disease as covariates, because donor is confounded with disease. However you could apply a donor random effect, eg,

zlm(~ disease + (1| donor), method = 'glmer')

With sufficient donors, this would be the preferred model.