pbmc3k - KeyError: 'base'

[shachafl]

Following the pbmc3k tutorial I get an error: KeyError: 'base'
when executing the following cmd:

sc.tl.rank_genes_groups(adata, 'leiden', groups=['0'], reference='1', method='wilcoxon')

I run python 3.8 in a venv on Ubuntu 20.04 (VM)

scanpy==1.9.3

More error details (notebook cell's output):

ranking genes
---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
Cell In[47], line 1
----> 1 sc.tl.rank_genes_groups(adata, 'leiden', groups=['0'], reference='1', method='wilcoxon')
      2 sc.pl.rank_genes_groups(adata, groups=['0'], n_genes=20)

File .../lib/python3.8/site-packages/scanpy/tools/_rank_genes_groups.py:590, in rank_genes_groups(adata, groupby, use_raw, groups, reference, n_genes, rankby_abs, pts, key_added, copy, method, corr_method, tie_correct, layer, **kwds)
    580 adata.uns[key_added] = {}
    581 adata.uns[key_added]['params'] = dict(
    582     groupby=groupby,
    583     reference=reference,
   (...)
    587     corr_method=corr_method,
    588 )
--> 590 test_obj = _RankGenes(adata, groups_order, groupby, reference, use_raw, layer, pts)
    592 if check_nonnegative_integers(test_obj.X) and method != 'logreg':
    593     logg.warning(
    594         "It seems you use rank_genes_groups on the raw count data. "
    595         "Please logarithmize your data before calling rank_genes_groups."
    596     )

File .../lib/python3.8/site-packages/scanpy/tools/_rank_genes_groups.py:93, in _RankGenes.__init__(self, adata, groups, groupby, reference, use_raw, layer, comp_pts)
     82 def __init__(
     83     self,
     84     adata,
   (...)
     90     comp_pts=False,
     91 ):
---> 93     if 'log1p' in adata.uns_keys() and adata.uns['log1p']['base'] is not None:
     94         self.expm1_func = lambda x: np.expm1(x * np.log(adata.uns['log1p']['base']))
     95     else:

KeyError: 'base'

[flying-sheep]

Duplicate of scverse/anndata#673

I’ll close this one, as the other one has a more complete description