Hi! I am currently working with a liver scRNA-seq dataset and trying to annotate my cells with scmap. I want to use the ex vivo dataset found here as a reference (https://www.livercellatlas.org/download.php). I found out there is batch effect within the reference dataset after doing some analysis. So here are my questions.

  Will this batch effect affect my annotation result or is the resulting centroid calculated by scmap still going to give a good representation of the cell type?

  If it has an effect, I should do data integration first and annotate the cells based on the corrected normalized count, right?