KeyError: "Values ['HLA-DQB1'], from ['HLA-DQB1'], are not valid obs/ var names or indices."

[ChenPeizhan]

Dear developers,
Thank you so much for providing such useful method, I met an issue when I run the sdm.spatialdm_local(subset, n_perm=99, method='z-score', specified_ind=None, nproc=1) step:

sdm.spatialdm_local(subset, n_perm=99, method='z-score', specified_ind=None, nproc=1) # local spot selection

---

KeyError Traceback (most recent call last)
Cell In[167], line 1
----> 1 sdm.spatialdm_local(subset, n_perm=99, method='z-score', specified_ind=None, nproc=1) # local spot selection

File ~/miniconda3/envs/omicversev17/lib/python3.11/site-packages/spatialdm/main.py:237, in spatialdm_local(adata, n_perm, method, specified_ind, nproc, scale_X)
235 ## different approaches
236 with threadpool_limits(limits=nproc, user_api='blas'):
--> 237 spot_selection_matrix(adata, ligand, receptor, ind, n_perm, method, scale_X)

File ~/miniconda3/envs/omicversev17/lib/python3.11/site-packages/spatialdm/utils.py:190, in spot_selection_matrix(adata, ligand, receptor, ind, n_perm, method, scale_X)
188 from scipy.stats.mstats import gmean
189 L1 = [pd.Series(x[0]).dropna().values for x in ligand.values]
--> 190 L_mat0 = [raw_norm[:, L1[l]].X.toarray().astype(np.float64)[:, 0] for l in range(len(L1))]
191 for i, k in enumerate(ligand.index):
192 if len(ligand.loc[k].dropna()) > 1:

File ~/miniconda3/envs/omicversev17/lib/python3.11/site-packages/spatialdm/utils.py:190, in (.0)
188 from scipy.stats.mstats import gmean
189 L1 = [pd.Series(x[0]).dropna().values for x in ligand.values]
--> 190 L_mat0 = [raw_norm[:, L1[l]].X.toarray().astype(np.float64)[:, 0] for l in range(len(L1))]
191 for i, k in enumerate(ligand.index):
192 if len(ligand.loc[k].dropna()) > 1:

File ~/miniconda3/envs/omicversev17/lib/python3.11/site-packages/anndata/_core/anndata.py:1011, in AnnData.getitem(self, index)
1009 def getitem(self, index: Index) -> AnnData:
1010 """Returns a sliced view of the object."""
-> 1011 oidx, vidx = self._normalize_indices(index)
1012 return AnnData(self, oidx=oidx, vidx=vidx, asview=True)

File ~/miniconda3/envs/omicversev17/lib/python3.11/site-packages/anndata/_core/anndata.py:992, in AnnData._normalize_indices(self, index)
991 def _normalize_indices(self, index: Index | None) -> tuple[slice, slice]:
--> 992 return _normalize_indices(index, self.obs_names, self.var_names)

File ~/miniconda3/envs/omicversev17/lib/python3.11/site-packages/anndata/_core/index.py:33, in _normalize_indices(index, names0, names1)
31 ax0, ax1 = unpack_index(index)
32 ax0 = _normalize_index(ax0, names0)
---> 33 ax1 = _normalize_index(ax1, names1)
34 return ax0, ax1

File ~/miniconda3/envs/omicversev17/lib/python3.11/site-packages/anndata/_core/index.py:111, in _normalize_index(indexer, index)
106 not_found = indexer[positions < 0]
107 msg = (
108 f"Values {list(not_found)}, from {list(indexer)}, "
109 "are not valid obs/ var names or indices."
110 )
--> 111 raise KeyError(msg)
112 return positions # np.ndarray[int]
113 msg = f"Unknown indexer {indexer!r} of type {type(indexer)}"

KeyError: "Values ['HLA-DQB1'], from ['HLA-DQB1'], are not valid obs/ var names or indices."

After I check the var.names in the AnnData, I could find the var_names in it. Can you help me to check this?

Thank you so much.