I would like to compare two groups (cell populations), from two different RNAseq experiments (sets). However, there are no overlapping groups in both experiments available, so an analysis in limma with batch effect (block design) is not possible. Let's say I have populations a, b, and c in experiment 1, and d, and e in experiment 2, and I would like to compare a with d.
Is there another way to compare the two populations in a sound manner? Or is it only possible to make a heatmap? And compare average cpm values?