Hi bioconductor community,

I have a question regarding covariates. We have performed RNA seq for two groups in which there are no females in control group Males (20) but we have females (5) in cases and males (20). The people who have carried out the experiments were reluctant in removing females. But is it the right way to include or are there any other alternatives to do differential gene expression analysis.

I would probably just do the M vs M analysis. You could instead include a term for sex and have a model with all 45 samples, but the M vs M analysis would be my preference for simplicity.