Has anyone seen an MA/MD plot like this? It’s for a mutant (QV) vs WT (N2). Distribution for up-regulated looks typical, but it looks like there there is a large group of genes commonly downregulated by about -1.7 log2. Used Bowtie2, featureCounts, and Edger (defaults) except excluded genes without CPM at least 2 in 1/2 of biological replicates.
Before I think too much about the biological explanation, I want to be able to rule out an analysis artifact.
The MA/MD plots for drug/no drug using the same pipeline and data have the typical fan shape.