alphapepttools.tl.diff_exp_ebayes

alphapepttools.tl.diff_exp_ebayes#

alphapepttools.tl.diff_exp_ebayes(adata, between_column, comparison, min_valid_values=2)#

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)

  • min_valid_values (int, optional) – Minimum number of valid (non-missing) values required in at least one group. By default 2.

Return type:

tuple[str, DataFrame]

Returns:

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

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