I am using DESeq2 for analyzing an RNASeq Experiment. The details of the setup are as follows:
I have two treatments for which I want to test for differential expression. However, when inspecting the data, the variability of the counts in one treatment group is considerably higher than the variability in the other group (for same mean).
If I understand the DESeq2 documentation correctly, the DESeq function fits one dispersion parameter per gene, not allowing for sample groups with different dispersion.
a) Is this understanding correct?
b) Is there a way to allow for sample-group specific dispersions? In a linear model setting, this would usually be achieved by setting different weights for the samples in different groups.