My sc-RNAseq on sponge larvae cells was done as 2 batches (library prepped separately, separate sequencing runs).
Samples consist of 7 cell types, 8 replicates each:
5 reps in batch 1 and 3 reps in batch 2; except for one cell type, which went to batch 2.
I use combat in the sva package to remove this known batch effect. However, it seems to have removed some of the wanted biological differences (difference between cell types):
I’m unable to back this up with by quoting the actual loss of DE genes after combat (I can’t do DESeq2 DE analysis on combat-ed counts as it’s normalised…?)
What do I do in this case? Is there a way to tweak the power of combat? This doesn't seem to mentioned in the vignette.
Admittedly, there are lots of noise in my data and if I run sva, I'll likely uncover other variables, but I wanna get rid of this known batch effect first.