Is it valid to compare multiple cell types by looking at the number of DEGs with q<0.05 between two conditions? Can this tell us which cell type shows the strongest effect?
For example, this was done in Allen et al, Cell, 2023, Fig. 4A (10.1016/j.cell.2022.12.010).
Aren’t cluster size or number of unique genes confounders in this analysis? Say cell type A with 5000 cells has much more DEGs than cells type B with only 200 cells. This was briefly touched here:
Does iterative random downsampling of the larger cluster help out here? Or are there other suggestions?
Advice is much appreciated!