ValueError: b'Extrapolation not allowed with blending' when using `"sc.pp.highly_variable_genes"` function about scanpy HOT 3 OPEN

Hey - it would be most helpful to post user questions in the scverse forum - there, other users encountering the same question will be able to find a response easier :)

Here, to take care of bugs in scanpy, it is most helpful for us if you are able to share public data/a small part of it/a synthetic data example so that we can check whats going on. Would it possible to you to supply something like that, such that I can reproduce your example myself?

From a first glance, with seurat_v3 requiring count data, it is important that your .X (becoming the layer you refer to as counts) indeed contains counts, otherwise loess quickly runs into stability issues.

from scanpy.

From a first glance, with seurat_v3 requiring count data, it is important that your .X (becoming the layer you refer to as counts) indeed contains counts, otherwise loess quickly runs into stability issues.

I would expect there would be a warning here if this were the case, since check_values defaults to True.

But at least this person had the same error caused by passing in normalized values:

• https://www.biostars.org/p/9535944/

The author of scikit-misc says:

pass surface="direct"

to the loess solver based only off the error message. So maybe we can enable that.

I don't know enough about loess to be able to say why that would fix this. It would be interesting to see the data that caused this error. I would definitely want to have a reproducible case before attempting a fix.

from scanpy.

My code also has the same bug problem, may I ask, how to solve it?

adata.raw = adata # keep full dimension safe sc.pp.highly_variable_genes( adata, flavor="seurat_v3",# n_top_genes=2000, layer="counts", batch_key="orig.ident", subset=True, span=1 )

Error output

`ValueError Traceback (most recent call last)
Cell In[13], line 3
1 #高变基因选取
2 adata.raw = adata # keep full dimension safe
----> 3 sc.pp.highly_variable_genes(
4 adata,
5 flavor="seurat_v3",#
6 n_top_genes=2000,
7 layer="counts",
8 batch_key="orig.ident",
9 subset=True,
10 span=1
11 )
13 filename = 'melanoma_sw_high_var.h5ad'
14 adata.write(filename)

File ~/miniconda3/envs/scanpy/lib/python3.12/site-packages/scanpy/preprocessing/_highly_variable_genes.py:441, in highly_variable_genes(adata, layer, n_top_genes, min_disp, max_disp, min_mean, max_mean, span, n_bins, flavor, subset, inplace, batch_key, check_values)
439 sig = signature(_highly_variable_genes_seurat_v3)
440 n_top_genes = cast(int, sig.parameters["n_top_genes"].default)
--> 441 return _highly_variable_genes_seurat_v3(
442 adata,
443 layer=layer,
444 n_top_genes=n_top_genes,
445 batch_key=batch_key,
446 check_values=check_values,
447 span=span,
448 subset=subset,
449 inplace=inplace,
450 )
452 if batch_key is None:
453 df = _highly_variable_genes_single_batch(
454 adata,
455 layer=layer,
(...)
462 flavor=flavor,
463 )

File ~/miniconda3/envs/scanpy/lib/python3.12/site-packages/scanpy/preprocessing/_highly_variable_genes.py:87, in _highly_variable_genes_seurat_v3(adata, layer, n_top_genes, batch_key, check_values, span, subset, inplace)
85 x = np.log10(mean[not_const])
86 model = loess(x, y, span=span, degree=2)
---> 87 model.fit()
88 estimat_var[not_const] = model.outputs.fitted_values
89 reg_std = np.sqrt(10**estimat_var)

File _loess.pyx:927, in _loess.loess.fit()

ValueError: b'Extrapolation not allowed with blending'`

from scanpy.