diff --git a/scanpy/tools/rank_genes_groups.py b/scanpy/tools/rank_genes_groups.py index d0118f9a86..9d3c693c7e 100644 --- a/scanpy/tools/rank_genes_groups.py +++ b/scanpy/tools/rank_genes_groups.py @@ -199,7 +199,7 @@ def rank_genes_groups( pvals[np.isnan(pvals)] = 1 # set Nan values to 1 to properly convert using Benhjamini Hochberg _, pvals_adj, _, _ = multipletests(pvals, alpha=0.05, method='fdr_bh') elif corr_method == 'bonferroni': - pvals_adj = pvals * n_genes + pvals_adj = np.minimum(pvals * n_genes, 1.0) scores_sort = np.abs(scores) if rankby_abs else scores partition = np.argpartition(scores_sort, -n_genes_user)[-n_genes_user:] @@ -302,7 +302,7 @@ def rank_genes_groups( pvals[np.isnan(pvals)] = 1 # set Nan values to 1 to properly convert using Benhjamini Hochberg _, pvals_adj, _, _ = multipletests(pvals, alpha=0.05, method='fdr_bh') elif corr_method == 'bonferroni': - pvals_adj = pvals * n_genes + pvals_adj = np.minimum(pvals * n_genes, 1.0) mean_rest[mean_rest == 0] = 1e-9 # set 0s to small value foldchanges = (means[imask] + 1e-9) / mean_rest @@ -358,7 +358,7 @@ def rank_genes_groups( pvals[np.isnan(pvals)] = 1 # set Nan values to 1 to properly convert using Benhjamini Hochberg _, pvals_adj, _, _ = multipletests(pvals, alpha=0.05, method='fdr_bh') elif corr_method == 'bonferroni': - pvals_adj = pvals * n_genes + pvals_adj = np.minimum(pvals * n_genes, 1.0) mean_rest[mean_rest == 0] = 1e-9 # set 0s to small value foldchanges = (means[imask] + 1e-9) / mean_rest