Hi there, I am using the most recent github version of scvi and have been running into this potential bug when I try to set up my data. It occurs when I use mudata or anndata.
Basically, it looks like something is happening in the setup that causes the function to cut off the column name of my batch/covariate variable at the first letter. Some other things that may help:
- Removing both the batch and covariate parameters resolves the bug. However, my data has strong batch effect, so I need to be able to use those parameters.
- Renaming my batch/covariate columns to be single-letter does actually get me a step further, but then I get a separate bug:
ValueError: Obsm ‘_scvi_extra_categorical_covs’ needs to be of one of <class ‘numpy.ndarray’>, <class ‘numpy.ma.core.MaskedArray’>, <class ‘scipy.sparse._csr.csr_matrix’>, <class ‘scipy.sparse._csc.csc_matrix’>, <class ‘scipy.sparse._csr.csr_array’>, <class ‘scipy.sparse._csc.csc_array’>, <class ‘h5py._hl.dataset.Dataset’>, <class ‘zarr.core.array.Array’>, <class ‘anndata.compat.ZappyArray’>, <class ‘anndata.abc.CSRDataset’>, <class ‘anndata.abc.CSCDataset’>, <class ‘anndata.compat.DaskArray’>, <class ‘anndata.compat.CupyArray’>, <class ‘anndata.compat.CupySparseMatrix’>, <class ‘anndata.compat.AwkArray’>, or <class ‘xarray.core.dataarray.DataArray’>, not <class ‘pandas.core.series.Series’>.I’m still trying to figure out how to get past this issue. - This entire step worked perfectly with the same data and parameters in an older version of scvi (1.2.2.post2), so it might be a dependency thing?
Does anyone know how I might go about fixing this? Thank you!