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[BUG] Errors saving `DeseqDataSet` to H5AD

Open jpintar opened this issue 1 year ago • 0 comments

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 avatar Mar 14 '24 15:03 jpintar