I have a question regarding the shape of my MA plot using deseq2. Basically I have two conditions that I am comparing (two types of blood cells within the mouse embryo), and three samples for each condition. I have noticed that in my dispersion, MA, and volcano plots there are a set of genes which are expressed in one condition but close to 0 in the other. I've included an MA plot after apeglm shrinkage, depicting that particular behavior. My suspicion is that it might be a closely related, contaminating/differentiating sub-population within the overall population that might be explaining these trends. I'm wondering whether any pre-filtering could be applied, or other techniques, that might be able to distentangle these genes from the overall analysis. I hope the explanation was ok, and thanks for any insight!