CODEWITHSUNDEEP
pythonscanpy
Raktim Gohain
Raktim Gohain

Reputation: 1

scanpy highly variable genes

filtering of highly variable genes using scanpy does not work in Windows. The same command has no issues while working with Mac.

sc.pp.highly_variable_genes(adata, layer = 'raw_data', n_top_genes = 4000, flavor = 'seurat_v3')

ImportError                               Traceback (most recent call last)
File ~\Anaconda3\lib\site-packages\scanpy\preprocessing\_highly_variable_genes.py:53, in _highly_variable_genes_seurat_v3(adata, layer, n_top_genes, batch_key, check_values, span, subset, inplace)
     52 try:
---> 53     from skmisc.loess import loess
     54 except ImportError:

File ~\AppData\Roaming\Python\Python39\site-packages\skmisc\loess\__init__.py:51, in <module>
      1 """
      2 =================================================
      3 Locally-weighted regression (:mod:`skmisc.loess`)
   (...)
     49    pp. 829--836. 1979.
     50 """
---> 51 from ._loess import (loess, loess_model, loess_inputs, loess_control,
     52                      loess_outputs, loess_prediction,
     53                      loess_confidence_intervals, loess_anova)
     56 __all__ = ['loess', 'loess_model', 'loess_control', 'loess_inputs',
     57            'loess_model', 'loess_outputs', 'loess_prediction',
     58            'loess_confidence_intervals', 'loess_anova']

ImportError: DLL load failed while importing _loess: The specified module could not be found.

During handling of the above exception, another exception occurred:

ImportError                               Traceback (most recent call last)
Input In [7], in <cell line: 1>()
----> 1 sc.pp.highly_variable_genes(adata, layer = 'raw_data', n_top_genes = 4000, flavor = 'seurat_v3')

File ~\Anaconda3\lib\site-packages\scanpy\preprocessing\_highly_variable_genes.py:422, 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)
    416     raise ValueError(
    417         '`pp.highly_variable_genes` expects an `AnnData` argument, '
    418         'pass `inplace=False` if you want to return a `pd.DataFrame`.'
    419     )
    421 if flavor == 'seurat_v3':
--> 422     return _highly_variable_genes_seurat_v3(
    423         adata,
    424         layer=layer,
    425         n_top_genes=n_top_genes,
    426         batch_key=batch_key,
    427         check_values=check_values,
    428         span=span,
    429         subset=subset,
    430         inplace=inplace,
    431     )
    433 if batch_key is None:
    434     df = _highly_variable_genes_single_batch(
    435         adata,
    436         layer=layer,
   (...)
    443         flavor=flavor,
    444     )

File ~\Anaconda3\lib\site-packages\scanpy\preprocessing\_highly_variable_genes.py:55, in _highly_variable_genes_seurat_v3(adata, layer, n_top_genes, batch_key, check_values, span, subset, inplace)
     53     from skmisc.loess import loess
     54 except ImportError:
---> 55     raise ImportError(
     56         'Please install skmisc package via `pip install --user scikit-misc'
     57     )
     58 df = pd.DataFrame(index=adata.var_names)
     59 X = adata.layers[layer] if layer is not None else adata.X

ImportError: Please install skmisc package via `pip install --user scikit-misc

That error is wrong becasue scikit-misc is already installed and requirements fulfilled.

Upvotes: 0

Views: 884

Answers (1)

YotamW Constantini
YotamW Constantini

Reputation: 410

This is an issue with skmisc, according to this you should "try installing numpy+mkl before any other packages"

Upvotes: 0

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