I have RNA seq data (paired end) isolated from exosomes from healthy and disease and have performed diff express using DESeq2. However, I have unusual skweing in my MA plot. I have not come accorss this before in any of my other experiments (or in the microvesicles from the same donors). There are 2984 DE genes. I was wondering whether this could be a consequence of uneven amounts of mRNA per vesicle? If so, what would be the best way to handle data of this type?
I noticed that someone else had an issue similar to this: DESeq2 MA plot of encode data