Hello,

I would like to try MOFA+ for some CITE-Seq data and I was wondering if you could provide some recommendations on how to deal with batch effects.
We‘re generally working with data derived from 2-3 different experiments, between which we observe minor batch effects for the RNA component and quite significant batch effects for the surface protein component.

I‘ve found that fastMNN gives good batch corrected PCA-like embeddings, but the reconstructed counts should be used with caution, as they can have negative values.
I saw that your FAQ mentions limma, but if I recall benchmarks generally show inferior batch correcting abilities when it comes to single-cell data.

Any insights or recommendations would be much appreciated, thanks!