Hi Folks, this is a conceptual question:
I have a RNA-seq dataset where I am trying to make comparisons among 3 levels of a factor - two parental genotypes and an F1. In addition to asking whether there is pairwise DE between genotypes (simple using contrast arguments in results), I would like to ask whether the F1 is intermediate between the two parents. This test is usually accomplished by comparing the mid-parent value (the estimate of the parental means) to the distribution of expression values of the F1. Is there a way to implement this test in DESeq2 - perhaps by setting a contrast between a value (mid parent mean) and the F1 count distribution?
Postdoctoral Fellow, UT Austin.