I’m trying to score a list of genes in my integrated dataset by running the following code:
my_gene = pd.read_csv("/home/unix/marieb/regev_lab_cell_cycle_genes.txt")
sc.tl.score_genes(adata, gene_list=my_gene, score_name=‘my_score’)
But I get the following error:
ValueError Traceback (most recent call last)
----> 1 sc.tl.score_genes(adata, gene_list=my_gene, score_name=‘my_score’)
~/.local/lib/python3.8/site-packages/scanpy/tools/_score_genes.py in score_genes(adata, gene_list, ctrl_size, gene_pool, n_bins, score_name, random_state, copy, use_raw)
113 if len(gene_list) == 0:
→ 114 raise ValueError(“No valid genes were passed for scoring.”)
116 if gene_pool is None:
ValueError: No valid genes were passed for scoring.
Please help me try to understand why this error comes up
It happens also when I try to set my gene list as something as simple as my_genes = [‘APOD’, ‘OLIG2’], which I know are expressed in my integrated dataset.