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Fix KeyError in statistical analysis helper for large datasets #227

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Fix KeyError in statistical analysis helper for large datasets #227

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5 changes: 4 additions & 1 deletion cellphonedb/src/core/methods/cpdb_statistical_analysis_helper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -782,7 +782,10 @@ def add_multidata_and_means_to_counts(counts: pd.DataFrame, genes: pd.DataFrame,

counts_relations = counts[['id_multidata', 'ensembl', 'gene_name', 'hgnc_symbol']].copy()

counts.set_index('id_multidata', inplace=True, drop=True)
# Manually set index to avoid issues with large DataFrames and set_index
counts.index = counts['id_multidata']
counts.index.name = 'id_multidata'

counts = counts[cells_names]
if np.any(counts.dtypes.values != np.dtype('float32')):
counts = counts.astype(np.float32)
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