sc.tl.score_genes -- ValueError: No valid genes were passed for scoring

[xyang2uchicago]

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?

I have found this issue in both old versions 1.9.3, 1.9.8 and the newest version 1.10.3.
I am pretty sure my gene names are in the adata.var_names (see below code).
I also confirm that each gene-set has 2 or more genes.
Can anyone help to debug?

Thank you,
Holly

Minimal code sample

print(sc.__version__)
# 1.10.3

# Randomly select 1000 cell indices
selected_cells = np.random.choice(adata.obs.index, size=1000, replace=False)
# Create a subset AnnData object
subset_adata = adata[selected_cells].copy()
subset_adata.write(save_fold + "subset_adata.h5ad")

#subset_known_markers = dict(list(filtered_known_markers.items())[:2])
tmp = ['Isl1', 'Tcf21', 'Tlx1'] 
[gene for gene in tmp if gene in subset_adata.var_names] == tmp  # True
tmp = ['Gata4', 'Nkx2-5', 'Nr2f2', 'Osr1', 'Tbx5', 'Wnt2'] 
[gene for gene in tmp if gene in subset_adata.var_names] == tmp  # True
subset_known_markers = {
    'Anterior cardiopharyngeal progenitors_Imaz2024': ['Isl1', 'Tcf21', 'Tlx1'], 
    'Cardiomyocytes FHF 1_Imaz2024': ['Gata4', 'Nkx2-5', 'Nr2f2', 'Osr1', 'Tbx5', 'Wnt2']
}
    
tmp = sc.tl.score_genes(subset_adata, gene_list= subset_known_markers, copy=True 
        #,use_raw=True 
        #,n_bins = 150 , ctrl_size =100
        )    # ctrl_size = 50 by default ; n_bins = 25 by default

Error output

WARNING: genes are not in var_names and ignored: ['Anterior cardiopharyngeal progenitors_Imaz2024', 'Cardiomyocytes FHF 1_Imaz2024']
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/project/xyang2/anaconda/py38/lib/python3.8/site-packages/scanpy/tools/_score_genes.py", line 115, in score_genes
    raise ValueError("No valid genes were passed for scoring.")
ValueError: No valid genes were passed for scoring.

Versions

-----
anndata     0.9.2
scanpy      1.9.3
-----
PIL                 10.4.0
cloudpickle         3.0.0
cycler              0.12.1
cython_runtime      NA
cytoolz             0.12.3
dask                2023.5.0
dateutil            2.9.0.post0
h5py                3.11.0
igraph              0.11.6
importlib_resources NA
jinja2              3.1.4
joblib              1.4.2
kiwisolver          1.4.7
leidenalg           0.10.2
llvmlite            0.41.1
lz4                 4.3.3
markupsafe          2.1.5
matplotlib          3.7.5
mpl_toolkits        NA
natsort             8.4.0
numba               0.58.1
numexpr             2.8.6
numpy               1.24.4
packaging           24.1
pandas              2.0.3
psutil              6.0.0
pyarrow             17.0.0
pyparsing           3.1.4
pytz                2024.2
scipy               1.10.1
session_info        1.0.0
six                 1.16.0
sklearn             1.3.2
tblib               3.0.0
texttable           1.7.0
threadpoolctl       3.5.0
tlz                 0.12.3
toolz               0.12.1
typing_extensions   NA
yaml                6.0.2
zipp                NA
-----
Python 3.8.19 | packaged by conda-forge | (default, Mar 20 2024, 12:47:35) [GCC 12.3.0]
Linux-4.18.0-305.3.1.el8.x86_64-x86_64-with-glibc2.10
-----
Session information updated at 2024-09-26 13:44