I saw a recent post by Michael Love (C: differential expression analysis of cell subtypes mixture) about the DeSeq2 function unmix() and I had a follow-up question (but did not want to hijack the original poster's question with one of my own.)
Could unmix() be used if you only know the expression profile of one of the "pure" populations but not the other? For instance my Tissue A sample, which has never been characterized before, unfortunately has a little bit of the well characterized Tissue B contaminating it...
Specifically, I have a bulk RNA seq data set where we enriched for a subset of epithelial cells in three different tissues, but we were not able to get 100% purity due to technical limitations/cell quantity and viability constraints which prevent us from doing flow sorting.
So now it is throwing off some of the differential expression analyses because genes expressed in the contaminating tissue type is showing up with high logFCs/low FDRs because they are expressed in one sample type but not at all in the others. It may be a hopeless cause and we will just have to be cautious in interpreting the data we have, but unmix() sounded like it could be a possibility.