My experiment set up: 2 samples from WT mice, 2 samples from KO mice, all sequenced with 10x 3' scRNA-seq. The cell populations sorted for sequencing are the same.
Seurat offers the anchor transfer method to perform dimension reduction and clustering, but differential expression is still performed upon normalized, untransformed data matrices.
Therefore, I was wondering if there are methods available to perform batch correction that can be used in differential expression. I would appreciate it if you could share your experience in dealing with this type of situation.
Thanks a lot~