highly_variable_genes AssertionError: Don’t call _normalize_index with non-categorical/string names
See original GitHub issueHi, I am using anndata 0.6.21 and scanpy 1.4.3 I executed this code:
sc.pp.highly_variable_genes(adata, min_mean=0.0001, max_mean=3, min_disp=0.5)
sc.pl.highly_variable_genes(adata)
adata = adata[:, adata.var['highly_variable']]
and I got this error:
AssertionError: Don’t call _normalize_index with non-categorical/string names
Can you help me?
Thank you.
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- Created 4 years ago
- Comments:9 (5 by maintainers)
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I had the same problem when I loaded sample data from a csv as a data frame and assigned it to adata.obs = df
Solution here is
adata.obs.index = adata.obs.index.astype(str). Should be called by default if this assertionerror is raised.