ValueError in score_genes_for_marginals Despite Matching Genes in Gene List

[pooji-96]

Hello,

I am encountering a ValueError when running the score_genes_for_marginals function, despite the fact that the genes in my list match several valid genes in the dataset. When I check the gene list, the genes do match those present in adata.var_names.

stp = stp.score_genes_for_marginals(gene_set_proliferation = "mouse", gene_set_apoptosis = "mouse")

WARNING: genes are not in var_names and ignored: Index(['Anln', 'Anp32e', 'Atad2', 'Aurka', 'Aurkb', 'Birc5', 'Blm', 'Brip1',
'Bub1', 'Casp8ap2', 'Cbx5', 'Ccnb2', 'Ccne2', 'Cdc20', 'Cdc25c',
'Cdc45', 'Cdc6', 'Cdca2', 'Cdca3', 'Cdca7', 'Cdca8', 'Cdk1', 'Cenpa',
'Cenpe', 'Cenpf', 'Chaf1b', 'Ckap2', 'Ckap2l', 'Ckap5', 'Cks1b', 'Cks2',
'Clspn', 'Ctcf', 'Dlgap5', 'Dscc1', 'Dtl', 'E2f8', 'Ect2', 'Exo1',
'Fam64a', 'Fen1', 'G2e3', 'Gas2l3', 'Gins2', 'Gmnn', 'Gtse1', 'Hells',
'Hjurp', 'Hmgb2', 'Hmmr', 'Hn1', 'Kif11', 'Kif20b', 'Kif23', 'Kif2c',
'Lbr', 'Mcm2', 'Mcm4', 'Mcm5', 'Mcm6', 'Mki67', 'Mlf1ip', 'Msh2',
'Nasp', 'Ncapd2', 'Ndc80', 'Nek2', 'Nuf2', 'Nusap1', 'Pcna', 'Pola1',
'Pold3', 'Prim1', 'Psrc1', 'Rad51', 'Rad51ap1', 'Rangap1', 'Rfc2',
'Rpa2', 'Rrm1', 'Rrm2', 'Slbp', 'Smc4', 'Tacc3', 'Tipin', 'Tmpo',
'Top2a', 'Tpx2', 'Ttk', 'Tubb4b', 'Tyms', 'Ube2c', 'Ubr7', 'Uhrf1',
'Ung', 'Usp1', 'Wdr76'],
dtype='object')

---

ValueError Traceback (most recent call last)
Cell In[16], line 1
----> 1 stp = stp.score_genes_for_marginals(gene_set_proliferation = "mouse", gene_set_apoptosis = "mouse")

File ~/.local/lib/python3.11/site-packages/moscot/base/problems/birth_death.py:108, in BirthDeathMixin.score_genes_for_marginals(self, gene_set_proliferation, gene_set_apoptosis, proliferation_key, apoptosis_key, **kwargs)
106 gene_set_proliferation = proliferation_markers(gene_set_proliferation) # type: ignore[arg-type]
107 if gene_set_proliferation is not None:
--> 108 sc.tl.score_genes(self.adata, gene_set_proliferation, score_name=proliferation_key, **kwargs)
109 self.proliferation_key = proliferation_key
110 else:

File ~/.local/lib/python3.11/site-packages/legacy_api_wrap/init.py:80, in legacy_api..wrapper..fn_compatible(*args_all, **kw)
77 @wraps(fn)
78 def fn_compatible(*args_all: P.args, **kw: P.kwargs) -> R:
79 if len(args_all) <= n_positional:
---> 80 return fn(*args_all, **kw)
82 args_pos: P.args
83 args_pos, args_rest = args_all[:n_positional], args_all[n_positional:]

File ~/.local/lib/python3.11/site-packages/scanpy/tools/_score_genes.py:134, in score_genes(adata, gene_list, ctrl_size, gene_pool, n_bins, score_name, random_state, copy, use_raw)
132 logg.warning(f"genes are not in var_names and ignored: {genes_to_ignore}")
133 if len(gene_list) == 0:
--> 134 raise ValueError("No valid genes were passed for scoring.")
136 if gene_pool is None:
137 gene_pool = pd.Index(var_names, dtype="string")

ValueError: No valid genes were passed for scoring.

I would appreciate any guidance on why this might be happening.

[MUCDK]

Hi @pooji-96 ,

We will look into this!
Would you mind posting a small reproducible example?

[selmanozleyen]

Yes @pooji-96 also any details regarding your version would be super helpful. Can you also print your var_names so we can compare?

[pooji-96]

Hello @MUCDK and @selmanozleyen,

Thank you both for your responses! I have attached the code file for your reference, which outlines the steps I have followed using Moscot on the dataset I am working with.
I have also attached a file containing the list of var_names from the dataset for comparison.
Additionally, I am using Moscot version 0.3.5 in the code. Let me know if you need any other details.
Looking forward to your feedback!
adata.var_names.txt
adata1.var_names.txt
Code.txt

[LeonStadelmann]

Hey @pooji-96 , thanks for providing your code!
Have you tried setting use_raw=False, so using stp = stp.score_genes_for_marginals(gene_set_proliferation = "mouse", gene_set_apoptosis = "mouse", use_raw=False) instead? Just to rule out any issues with the anndata object similiar to this one: scverse/scanpy#3266.

[pooji-96]

Hello @LeonStadelmann ,
I haven't tried that yet, but I'll run it and see if it helps. Thanks for the suggestion!