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[BUG] Errors saving DeseqDataSet to H5AD #254

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jpintar opened this issue Mar 14, 2024 · 0 comments
Open

[BUG] Errors saving DeseqDataSet to H5AD #254

jpintar opened this issue Mar 14, 2024 · 0 comments
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@jpintar
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jpintar commented Mar 14, 2024

When I attempt to save my DeseqDataSet AnnData object to H5AD, errors are thrown becuase

  1. dds.varm['replaced']
  2. dds.uns['trend_coeffs']

are stored as a pandas.core.series.Series, which cannot be written to H5AD in those positions. Calling

  1. dds.varm['replaced'] = dds.varm['replaced'].values
  2. dds.uns['trend_coeffs'] = dds.uns['trend_coeffs'].to_dict()

before dds.write_h5ad(<path>) resolved the issue without loss of functionality.

PyDESeq2 version 0.4.7 on CentOS 7.
@jpintar jpintar added the bug Something isn't working label Mar 14, 2024
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