I am analyzing differential gene expression from an RNA-Seq experiment in which two factors were applied. I have multiple replicates among samples when just Factor 1 is considered, and there is significant clustering among the groups. When Factor 2 is considered as well, there is one group that has no replicates of Factor 2 at a certain level of Factor 1, while the other levels of Factor 1 have 2 replicates for each level of Factor 2. I have good reason not to discard the group with no replicates, because the annotated set of differentially expressed genes strongly indicates the effect of Factor 2 is significant.
My question is, do I need to do anything special with respect to the dispersion factor, or will the factor derived from the replicated samples be applied to the group lacking replicates? Thanks!