I downloaded some publicly available RNA-seq data and want to compare those samples carrying a mutation (~4) against the rest (~800!). I ran both EdgeR and DESeq2, and the first results in an asymmetric volcano plot: skewed in one of the sides, meaning that it results in very large logFC that have large (NS) adjusted p-values. So next, in order to see if this asymmetry is persistant, I ran several random partitions of the data as groups (but keeping them highly unbalanced), obtaining the same behavior. Here an example of what I mean (I run it with 4, 20 and 100 to show how this effect decreases as I increase the small class size)
*I tried EdgeR-robust and I still get the same effect.
I do not see this effect when running DESeq2, only very few DE genes. What method would you recommend using when comparing such different class sizes?