Batch-Specific Training for Doublet Removal

Hi all,

I’m working on an scRNAseq project and I’m trying to investigate different packages to remove doublets in python. My initial dataset has 6 batches that are all for the same region of tissue.

As I understand it, I need to first convert my AnnData object to a scvi model, train the scvi model, convert the scvi model to a solo model per batch, and then train each solo model to get predictions for doublets.

Before I try to run scvi & solo on large quantities, I wanted to confirm that the scvi.model.scvi.setup_anndata function was designed for multiple batches with the batch_key argument, but that the scvi.external.SOLO.from_scvi_model function was intended to be run on one batch at a time using the same scvi model to start. Also, any explanation as to why it works (or doesn’t) work this way would be helpful.