Error when running sc.tl.rank_genes_groups

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• (optional) I have confirmed this bug exists on the main branch of scanpy.

What happened?

Hello, I got an error when trying to run sc.tl.rank_genes_groups on xenium data. The error message show below:
Could you please help? Thank you very much

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[134], [line 1](vscode-notebook-cell:?execution_count=134&line=1)
----> [1](vscode-notebook-cell:?execution_count=134&line=1) sc.tl.rank_genes_groups(adata_tcell, 'Enriched_Factor', method='t-test', key_added = "t-test")
      [2](vscode-notebook-cell:?execution_count=134&line=2) sc.pl.rank_genes_groups(adata_tcell, n_genes=25, sharey=False, key = "t-test")
      [4](vscode-notebook-cell:?execution_count=134&line=4) # results are stored in the adata.uns["t-test"] slot

File /opt/anaconda3/envs/istar2/lib/python3.9/site-packages/legacy_api_wrap/__init__.py:80, in legacy_api.<locals>.wrapper.<locals>.fn_compatible(*args_all, **kw)
     [77](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/istar2/lib/python3.9/site-packages/legacy_api_wrap/__init__.py:77) @wraps(fn)
     [78](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/istar2/lib/python3.9/site-packages/legacy_api_wrap/__init__.py:78) def fn_compatible(*args_all: P.args, **kw: P.kwargs) -> R:
     [79](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/istar2/lib/python3.9/site-packages/legacy_api_wrap/__init__.py:79)     if len(args_all) <= n_positional:
---> [80](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/istar2/lib/python3.9/site-packages/legacy_api_wrap/__init__.py:80)         return fn(*args_all, **kw)
     [82](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/istar2/lib/python3.9/site-packages/legacy_api_wrap/__init__.py:82)     args_pos: P.args
     [83](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/istar2/lib/python3.9/site-packages/legacy_api_wrap/__init__.py:83)     args_pos, args_rest = args_all[:n_positional], args_all[n_positional:]

File /opt/anaconda3/envs/istar2/lib/python3.9/site-packages/scanpy/tools/_rank_genes_groups.py:682, in rank_genes_groups(adata, groupby, mask_var, use_raw, groups, reference, n_genes, rankby_abs, pts, key_added, copy, method, corr_method, tie_correct, layer, **kwds)
    [679](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/istar2/lib/python3.9/site-packages/scanpy/tools/_rank_genes_groups.py:679) logg.debug(f"consider {groupby!r} groups:")
    [680](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/istar2/lib/python3.9/site-packages/scanpy/tools/_rank_genes_groups.py:680) logg.debug(f"with sizes: {np.count_nonzero(test_obj.groups_masks_obs, axis=1)}")
--> [682](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/istar2/lib/python3.9/site-packages/scanpy/tools/_rank_genes_groups.py:682) test_obj.compute_statistics(
    [683](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/istar2/lib/python3.9/site-packages/scanpy/tools/_rank_genes_groups.py:683)     method,
    [684](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/istar2/lib/python3.9/site-packages/scanpy/tools/_rank_genes_groups.py:684)     corr_method=corr_method,
    [685](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/istar2/lib/python3.9/site-packages/scanpy/tools/_rank_genes_groups.py:685)     n_genes_user=n_genes_user,
    [686](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/istar2/lib/python3.9/site-packages/scanpy/tools/_rank_genes_groups.py:686)     rankby_abs=rankby_abs,
    [687](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/istar2/lib/python3.9/site-packages/scanpy/tools/_rank_genes_groups.py:687)     tie_correct=tie_correct,
    [688](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/istar2/lib/python3.9/site-packages/scanpy/tools/_rank_genes_groups.py:688)     **kwds,
...
    [220](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/istar2/lib/python3.9/site-packages/numpy/matrixlib/defmatrix.py:220)         return N.dot(self, other)

File <__array_function__ internals>:180, in dot(*args, **kwargs)

ValueError: shapes (224,5090) and (224,5090) not aligned: 5090 (dim 1) != 224 (dim 0)

Minimal code sample

sc.tl.rank_genes_groups(adata_tcell, 'Enriched_Factor', method='t-test', key_added = "t-test")
sc.pl.rank_genes_groups(adata_tcell, n_genes=25, sharey=False, key = "t-test")

Error output

Versions

Start in scanpy/tools/_rank_genes_groups.py around rank_genes_groups and its compute_statistics call, then reproduce the minimal sc.tl.rank_genes_groups example. The report does not include versions or a reproducible dataset, so first determine whether the shape mismatch can be reproduced; done means identifying the cause and confirming the call no longer raises the reported ValueError.