I want to use scArches to query disease samples to a normal reference. My data comes from a range of studies, using different single cell technologies, each including different patient samples.
My reference model looks like this:
But when I add the query data I get an error:
vae_q = scvi.model.SCVI.load_query_data(
scArches currently does not support models with extra categorical covariates.
Does this mean I can’t have multiple covariates? Is there any workaround for this?