Hi, I am wondering if you applied any quality control filters on the validation and test set that were not applied on the training cells, i.e., if you filter out low quality cells?
Thanks!
Please find Broad’s response below:
We used the same filtering criterion for the train/validation/test sets: sc.pp.filter_cells(adata, min_counts=10) and sc.pp.filter_genes(adata, min_cells=5)