I’m new to Python, Scanpy, and Anndata, please let me know if I made any mistakes. This warning is really confusing me for a long time.

Background: I have downloaded a h5ad file from a dataset, and loaded it using Scanpy. I successfully read the h5ad file, but I found that its var_names contain gene_id, so I want to change var_names and var_names_make_unique().

import scanpy as sc
LW119 = sc.read_h5ad('/data/.../adata_LW119.h5ad')

 	                          feature 	                     symbol                  
ENSG00000243485_MIR1302-2HG 	ENSG00000243485_MIR1302-2HG 	MIR1302-2HG
ENSG00000237613_FAM138A 	ENSG00000237613_FAM138A 	FAM138A
ENSG00000186092_OR4F5 	ENSG00000186092_OR4F5 	OR4F5
ENSG00000238009_AL627309.1 	ENSG00000238009_AL627309.1 	AL627309.1
ENSG00000239945_AL627309.3 	ENSG00000239945_AL627309.3 	AL627309.3
... 	... 	...
ENSG00000277856_AC233755.2 	ENSG00000277856_AC233755.2 	AC233755.2
ENSG00000275063_AC233755.1 	ENSG00000275063_AC233755.1 	AC233755.1
ENSG00000271254_AC240274.1 	ENSG00000271254_AC240274.1 	AC240274.1
ENSG00000277475_AC213203.1 	ENSG00000277475_AC213203.1 	AC213203.1
ENSG00000268674_FAM231C 	ENSG00000268674_FAM231C 	FAM231C

33538 rows × 2 columns

LW119.var_names = LW119.var.symbol


 symbol 	           feature 	                    symbol
MIR1302-2HG 	ENSG00000243485_MIR1302-2HG 	MIR1302-2HG
FAM138A 	ENSG00000237613_FAM138A 	FAM138A
OR4F5 	ENSG00000186092_OR4F5 	OR4F5
AL627309.1 	ENSG00000238009_AL627309.1 	AL627309.1
AL627309.3 	ENSG00000239945_AL627309.3 	AL627309.3
... 	... 	...
AC233755.2 	ENSG00000277856_AC233755.2 	AC233755.2
AC233755.1 	ENSG00000275063_AC233755.1 	AC233755.1
AC240274.1 	ENSG00000271254_AC240274.1 	AC240274.1
AC213203.1 	ENSG00000277475_AC213203.1 	AC213203.1
FAM231C 	ENSG00000268674_FAM231C 	FAM231C

33538 rows × 2 columns

CategoricalIndex(['MIR1302-2HG', 'FAM138A', 'OR4F5', 'AL627309.1',
                  'AL627309.3', 'AL627309.2', 'AL627309.4', 'AL732372.1',
                  'OR4F29', 'AC114498.1',
                  'AC007325.2', 'BX072566.1', 'AL354822.1', 'AC023491.2',
                  'AC004556.1', 'AC233755.2', 'AC233755.1', 'AC240274.1',
                  'AC213203.1', 'FAM231C'],
                 categories=['A1BG', 'A1BG-AS1', 'A1CF', 'A2M', 'A2M-AS1', 'A2ML1', 'A2ML1-AS1', 'A2ML1-AS2', ...], ordered=False, dtype='category', name='symbol', length=33538)


TypeError                                 Traceback (most recent call last)
Cell In[22], line 1
----> 1 LW119.var_names_make_unique()

File /mnt/wangd/anaconda3/lib/python3.10/site-packages/anndata/_core/, in AnnData.var_names_make_unique(self, join)
   1892 def var_names_make_unique(self, join: str = "-"):
   1893     # Important to go through the setter so obsm dataframes are updated too
-> 1894     self.var_names = utils.make_index_unique(self.var.index, join)

File /mnt/wangd/anaconda3/lib/python3.10/site-packages/anndata/, in make_index_unique(index, join)
    251 if tentative_new_name not in values_set:
    252     values_set.add(tentative_new_name)
--> 253     values_dup[i] = tentative_new_name
    254     break
    255 issue_interpretation_warning = True

File /mnt/wangd/anaconda3/lib/python3.10/site-packages/pandas/core/arrays/, in NDArrayBackedExtensionArray.__setitem__(self, key, value)
    247 def __setitem__(self, key, value):
    248     key = check_array_indexer(self, key)
--> 249     value = self._validate_setitem_value(value)
    250     self._ndarray[key] = value

File /mnt/wangd/anaconda3/lib/python3.10/site-packages/pandas/core/arrays/, in Categorical._validate_setitem_value(self, value)
   1455     return self._validate_listlike(value)
   1456 else:
-> 1457     return self._validate_scalar(value)

File /mnt/wangd/anaconda3/lib/python3.10/site-packages/pandas/core/arrays/, in Categorical._validate_scalar(self, fill_value)
   1482     fill_value = self._unbox_scalar(fill_value)
   1483 else:
-> 1484     raise TypeError(
   1485         "Cannot setitem on a Categorical with a new "
   1486         f"category ({fill_value}), set the categories first"
   1487     )
   1488 return fill_value

TypeError: Cannot setitem on a Categorical with a new category (RGS5-1), set the categories first

Welcome, @wangda :raised_hands:

LW119.var_names = LW119.var.symbol.values.astype(str) should solve it for you — the index should have the string type.