Hello MAST team,

I would like to use MAST for testing differential expression between cells from two treatment groups. The data is from a nested factorial design, and I would like to know how to best take the structure of the data into account.

Each of the two treatment groups have cells from three different plates, and these plates are unique. Should I fit the data with a mixed model approach with the treatment as a fixed effect and the plate as a nested random effect? Something like this:

lmer.output <- zlm(~ Treatment +(1|Treatment:Plate), data,method='glmer', ebayes=FALSE)

followed by a likelihood ratio test for Treatment?

Or should I go for a fixed effects model with treatment-plate interactions, test the interactions, and if they are not significant refit the model without the plates?

Thank you for your time,

Darius