alphapepttools.tl.diff_exp_ebayes

alphapepttools.tl.diff_exp_ebayes#

alphapepttools.tl.diff_exp_ebayes(adata, between_column, comparison)#

Run Limma eBayes moderated ttest for differential expression

Parameters:

  • adata (ad.AnnData) – AnnData object with expression data in .X and sample metadata in .obs

  • between_column (str) – Column name in adata.obs containing the contrast levels

  • comparison (tuple) – Two levels to compare, meant to follow the convention (treatment, control)

Return type:

tuple[str, DataFrame]

Returns:

pd.DataFrame | None DataFrame with Limma eBayes differential expression results.

Notes

This implementation removes all features with any missing values to ensure compatibility with the inmoose Limma implementation. If features with missing values should be retained, their missing values must be imputed prior to running this function.

Contents