Table 5.

Batch effect correction comparison averaged over 32 simulation settings with balanced batches (500 cells in each batch), excluding settings where batch effect or cell type effects are zero.^a

Method	kBET Acceptance	1 - ASW Batch	ASW Cell Type	LISI Batch	1 - LISI Cell Type
Raw Data	0.000	0.634	0.104	0.006	0.866
JIVE	0.250	0.881	0.290	0.323	0.935
Seurat	0.317	0.976	0.158	0.462	0.878
Harmony	0.708	0.999	0.142	0.790	0.880
Liger	0.428	0.922	0.158	0.449	0.925
Combat-seq	0.104	1.000	–0.018	0.400	0.682

^aHigher values indicate better mixing of different batches or better retention of cell type effects. The highest average value for each metric is in bold. kBET results are based on a 5% sample size; results were similar at larger sample sizes.