AttributeError: Can only use .str accessor with string values!

[DUAN-GAO]

Please make sure these conditions are met

• I have checked that this issue has not already been reported.
• I have confirmed this bug exists on the latest version of scanpy.
• (optional) I have confirmed this bug exists on the main branch of scanpy.

What happened?

Dear scanpy teams, research fellows,
I downloaded some scRNA-seq data from https://zenodo.org/records/3357167,
and when I was tring to use anndata.AnnData.concatenate to combine two read count data(I checked their dimensions and the result were Baron_human: [2133,22758] and Segerstolpe: [8569,17500] which means they certainly have different annotated genes), I got below error.

Could u help. many thanks!!

Minimal code sample

all_adata = anndata.AnnData.concatenate(train_adata,test_adata)

Error output

  File "C:\Users\Administrator\AppData\Local\Programs\Python\Python310\lib\site-packages\pandas\core\strings\accessor.py", line 245, in _validate
    raise AttributeError("Can only use .str accessor with string values!")
AttributeError: Can only use .str accessor with string values!

Versions

>>> scanpy.logging.print_versions()
-----
anndata     0.8.0
scanpy      1.9.3
-----
CIForm              NA
PIL                 9.1.0
astunparse          1.6.3
cffi                1.15.1
colorama            0.4.6
cycler              0.10.0
cython_runtime      NA
dateutil            2.8.2
google              NA
h5py                3.11.0
igraph              0.10.4
joblib              1.2.0
kiwisolver          1.4.2
leidenalg           0.9.1
llvmlite            0.39.1
matplotlib          3.5.2
mpl_toolkits        NA
natsort             8.3.1
nt                  NA
numba               0.56.4
numpy               1.23.5
opt_einsum          v3.3.0
packaging           21.3
pandas              2.2.3
plotly              5.13.1
psutil              5.9.4
pyparsing           3.0.9
pytz                2022.1
scipy               1.10.0
session_info        1.0.0
six                 1.16.0
sklearn             1.2.1
texttable           1.6.7
threadpoolctl       3.1.0
torch               1.13.1+cpu
tqdm                4.64.1
typing_extensions   NA
yaml                6.0
zoneinfo            NA
zope                NA
-----
Python 3.10.4 (tags/v3.10.4:9d38120, Mar 23 2022, 23:13:41) [MSC v.1929 64 bit (AMD64)]
Windows-10-10.0.19041-SP0
-----
Session information updated at 2024-09-26 11:05

[flying-sheep]

Hi, please create a minimal reproducible example, including a complete stack trace of the error.

Mentioning which data set you used and the error message alone does not help us to figure out what happened, as we lack the context of both the steps you took that lead up to the error and where exactly in the code the error happened.

[DUAN-GAO]

I think the reason is Baron_human and Segerstolpe got different dimensions, which I printed out in the error. If so, how to fix it, many thanks.
code

x_Traindata_path = 'F:/迅雷下载/Intra-dataset/Pancreatic_data/Baron_human/'
Train_name = 'Baron'
Testdata_path = 'F:/迅雷下载/Intra-dataset/Pancreatic_data/Segerstolpe/'
Testdata_name = 'Segerstolpe'

import scanpy as sc

test_adata = sc.read_csv(Testdata_path + Testdata_name + ".csv")

train_adata = sc.read_csv(x_Traindata_path + Train_name + ".csv")

all_adata = sc.AnnData

all_adata = all_adata.concatenate(train_adata)
all_adata = all_adata.concatenate(test_adata)

error

AnnData object with n_obs × n_vars = 2133 × 22757
AnnData object with n_obs × n_vars = 8569 × 17499

  File "<stdin>", line 1, in <module>
  File "C:\Users\Administrator\AppData\Local\Programs\Python\Python310\lib\site-packages\anndata\_core\anndata.py", line 1806, in concatenate
    out.var.columns.str.extract(pat, expand=False)
  File "C:\Users\Administrator\AppData\Local\Programs\Python\Python310\lib\site-packages\pandas\core\accessor.py", line 224, in __get__
    accessor_obj = self._accessor(obj)
  File "C:\Users\Administrator\AppData\Local\Programs\Python\Python310\lib\site-packages\pandas\core\strings\accessor.py", line 191, in __init__
    self._inferred_dtype = self._validate(data)
  File "C:\Users\Administrator\AppData\Local\Programs\Python\Python310\lib\site-packages\pandas\core\strings\accessor.py", line 245, in _validate
    raise AttributeError("Can only use .str accessor with string values!")
AttributeError: Can only use .str accessor with string values!

[DUAN-GAO]

Also
scanpy == 1.10.0