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error in scanpy first tutorial

See original GitHub issue

Hi, I’m trying scanpy for the first time, but following the first tutorial I got the error below. Any idea of what is happening?

>>> filter_result = sc.pp.filter_genes_dispersion(
...     adata.X, min_mean=0.0125, max_mean=3, min_disp=0.5)
Traceback (most recent call last):
  File "<stdin>", line 2, in <module>
  File "/opt/anaconda3/envs/tiget/lib/python3.6/site-packages/scanpy/preprocessing/simple.py", line 328, in filter_genes_dispersion
    disp_std_bin[one_gene_per_bin] = disp_mean_bin[one_gene_per_bin]
  File "/opt/anaconda3/envs/tiget/lib/python3.6/site-packages/pandas/core/series.py", line 938, in __setitem__
    setitem(key, value)
  File "/opt/anaconda3/envs/tiget/lib/python3.6/site-packages/pandas/core/series.py", line 929, in setitem
    self._where(~key, value, inplace=True)
  File "/opt/anaconda3/envs/tiget/lib/python3.6/site-packages/pandas/core/generic.py", line 7539, in _where
    level=level, fill_value=np.nan)
  File "/opt/anaconda3/envs/tiget/lib/python3.6/site-packages/pandas/core/series.py", line 3248, in align
    broadcast_axis=broadcast_axis)
  File "/opt/anaconda3/envs/tiget/lib/python3.6/site-packages/pandas/core/generic.py", line 7366, in align
    fill_axis=fill_axis)
  File "/opt/anaconda3/envs/tiget/lib/python3.6/site-packages/pandas/core/generic.py", line 7435, in _align_series
    return_indexers=True)
  File "/opt/anaconda3/envs/tiget/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 3772, in join
    return_indexers=return_indexers)
  File "/opt/anaconda3/envs/tiget/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 4012, in _join_monotonic
    ridx = self._left_indexer_unique(sv, ov)
  File "pandas/_libs/join_helper.pxi", line 774, in pandas._libs.join.left_join_indexer_unique_object
ValueError: Buffer dtype mismatch, expected 'Python object' but got 'signed char'

Issue Analytics

State:
Created 5 years ago
Comments:9 (6 by maintainers)

Top GitHub Comments

1reaction

fidelramcommented, May 23, 2018

The solution do downgrade to pandas=0.22 worked for me. Thanks

0reactions

falexwolfcommented, May 23, 2018

I was wrong. The pandas 0.23 issue is not related to the prerelease… Unfortunately, I still haven’t found the time to figure out what is going wrong… but it’s on top of the list.