GPU available but not using

[adamgayoso]

@karenlawwc

I already filtered the adata so that protein and RNA share the same cells. The full traceback are below. Somehow the index of the adata is messed up and is throwing the error?

Issue will be fixed in the next release, but also check out my response here:

Questions about running differential expression

Ok I understand the issue. In the notebook you shared you can replace adata.obsm["protein_expression"] = mdata["adt"].layers["counts"].A.copy() with adata.obsm["protein_expression"] = mdata["adt"].to_df("counts") The issue arises due to the first line giving a numpy array, so our library generates integer based index for the protein names. This causes an issue with accessing a pandas series in your traceback. We will push a fix soon. In the meantime, the recommended workflow is to use data…