I have scRNA-seq data generated by Smart-seq2 which includes one plate of wild-type cells and a separate plate of knock-out cells. I would like to combine the data from these two plates in order to investigate any effects caused by the experimental intervention. I understand that plate and genotype are confounded in this design, but can fastMNN still be used to integrate such data? My approach would be to analyse the plates separately then merge them with fastMNN and re-do the dimensionality reduction and clustering so I can perform some comparative analyses. Are there any caveats or limitations to this approach that I should keep in mind?