Here is part(sorry, it's already shows what I want reflect) of my maplot

The relative distribution of all red point and black point are okay, what is different with normal MAplot is the global plot lower than we expected in general, I mean it's "roughly symmetry line" lower than y=0.

I checked my workflow, use res_diff, which get from res_diff <- results(dds2, pAdjustMethod = "BH")

I checked all what I can think of, still don't know what's wrong here?

Thanks for any view!