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[cellxgene] human_retina_cell_atlas dataset cannot be normalized #358

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KaiWaldrant opened this issue Feb 5, 2024 · 0 comments
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bug Something isn't working cellxgene_census Relates to cellxgene_census dataset dataset_loader Relates to a dataset_loader

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@KaiWaldrant
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KaiWaldrant commented Feb 5, 2024

Describe the bug
When trying to normalize the human_retina_cell_atlas dataset an error is raised:

Traceback (most recent call last):
  File "/tmp/nxf.AI6Hw8VUNe/.viash_script.sh", line 43, in
    lognorm = sc.pp.log1p(norm["X"])
  File "/usr/local/lib/python3.10/functools.py", line 889, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
  File "/usr/local/lib/python3.10/site-packages/scanpy/preprocessing/_simple.py", line 333, in log1p_sparse
    X = check_array(
  File "/usr/local/lib/python3.10/site-packages/sklearn/utils/validation.py", line 967, in check_array
    raise ValueError(
ValueError: Found array with 0 sample(s) (shape=(0, 0)) while a minimum of 1 is required.

https://tower.nf/orgs/openproblems-bio/workspaces/openproblems-bio/watch/2hClUahANEhEc0

@KaiWaldrant KaiWaldrant added bug Something isn't working dataset_loader Relates to a dataset_loader cellxgene_census Relates to cellxgene_census dataset labels Feb 5, 2024
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Labels
bug Something isn't working cellxgene_census Relates to cellxgene_census dataset dataset_loader Relates to a dataset_loader
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