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filter_rank_genes_groups fold change calculation

See original GitHub issue

filter_rank_genes_groups handles log values differently than the rank_genes_groups function. The discrepancy gives different DE gene lists when filtering genes based on log2fc_min=1 with get.rank_genes_groups_df vs min_fold_change=2 with tl.filter_rank_genes_groups

In rank_genes_groups, np.expm1 is used:

foldchanges = (np.expm1(means[imask]) + 1e-9) / (np.expm1(mean_rest) + 1e-9)

rankings_gene_logfoldchanges.append(np.log2(foldchanges[global_indices]))

In filter_rank_genes_groups, np.exp is used:

if log:
    fold_change_matrix.loc[:, cluster] = (np.exp(mean_obs.loc[True]) / np.exp(mean_obs.loc[False])).values

Issue Analytics

State:
Created 4 years ago
Reactions:2
Comments:9 (2 by maintainers)

Top GitHub Comments

1reaction

Koncopdcommented, Jul 31, 2020

@ivirshup yes, i’ll check.

0reactions

racngcommented, Jun 8, 2022

Looks like this has been fixed. There is an option now to compare absolute fold changes if you set compare_abs=True.

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