I have a couple sets of single-level RNA-seq experiments in which I'm identifying clusters of upregulated/downregulated genes across one treatment (ie. WT against KO). There are multiple biological replicates within each group - the problem is that there is in-group variance and the PCA shows that the two groups are not exactly linearly separable. In other words, the differences I'm looking for are probably subtle.
EDIT: I have been using DESeq2 to do differential gene expression analysis. My question is as follows:
Is there a way to cluster genes knowing that samples within a group should bear resemblance to one another? Ie. Find genes that are upregulated across all of the WT relative to all of the KOs? When I cluster them right now, the sample distances are sometimes so variable that the WT and KOs cluster together.
Forgive me if this is a really trivial question! Novice here.