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[cellxgene] human_retina_cell_atlas dataset cannot be normalized

Open KaiWaldrant opened this issue 2 years ago • 0 comments

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 avatar Feb 05 '24 13:02 KaiWaldrant