How to normalise scRNASeq data for differential expression analysis
I would suggest using a likelihood ratio test for differential expression using logistic regression with batch as a latent variable. In Seurat you can do:

markers &lt;- FindAllMarkers(object, test.use = 'LR', latent.vars = 'batch')

(change "object" and "batch" accordingly)

See https://www.biorxiv.org/content/early/2018/02/14/258566 from Lior Pachter's group for some more info on the LR test.