Hello, I am analysing data comparing transcriptomics of exosomes to cells and I am not sure if these results looks normal

1. I identified a lot more upregulated genes in exosomes than in cells (see volcano plots below). I think this is unusual for 2 reasons. one, I am not certain but I thought I should expect similar up and down regulated genes on a volcano plots, but this is very skewed. Two, exosome are a lot smaller than cells and is expected to contain less mRNA species than cells, but the result suggests that there are thousands of gene that are upregulated inside exosomes (I have double checked that my contrast was in the right order). One possible explanation is that the fewer mRNA species are enriched because they are actively selected and packaged into exosomes. Does this sound reasonable?

2. Here is the MA plot from the same dataset used for volcano plots. with ashr shrinkage (I need to use contrast, so I select this method for shrinkage) I wonder if this MA plots looks okay. They are slightly off center. If this is unusal what should I do to improve the normalisation? I tried removing more genes with low count but it did not help much. Other QC plots like bar plot, PCA, sample heatmaps and histogram looks fine.

3. Is the okay to proceed the downstream analysis of the DEGs if this is the MA plots/ volcano plots?

I think what you have to figure out here is which genes you want to normalize the dataset to. I guess (not my field) that exosomes are not just a copy of the cellular transcriptome but highly enriched (and depleted). I would first check where in that MA-plot common house keeping genes are. That then requires your biological knowledge. Do you expect house keeping genes in the exosomes, or can you use any other set of genes to base normalization on. You probably expect notable changes between the cell and exosome composition. Are there any spike-ins in the experiment? The MA-plot already tells that a lot is going on, and that it is not symmetrical.