Hello all, I have a general doubt, Can we use the edgeR and Limma model to do the subtype specific differntial expression analysis ? If not then what are the barriers for this and what else can be done to do the subtype specfic expression analysis??

Do you mean identifying cell subtype proportions dynamically from the expression data? No, limma and edgeR don't have built-in functionality to do that. They expect cell types to be pre-specified. You would need to use a deconvolution method.

limma and edgeR probably could be used if you knew the cell subtype proportions in each sample.