Extended Data Fig. 4. Benchmarking matrix-correction methods identifies limma as the best balance of batch removal and biological preservation.

(a) Signed changes relative to the uncorrected 917-protein matrix across nine metrics and ten correction methods. Positive values indicate improvement; batch average silhouette width (ASW) was sign-reversed so that higher values uniformly denote better performance. Metrics assessed batch removal (batch mixing, batch ASW and principal-component-regression batch reduction) or biological preservation (differential-abundance preservation, highly variable feature conservation, biology k-nearest-neighbour accuracy, biology ASW, graph connectivity and isolated-label ASW). (b) Direction-aware within-metric ranks, with rank 1 indicating the best-performing method. (c) Batch-removal, biological-preservation and composite scores. The composite score weighted biological preservation more strongly (0.4 × batch score + 0.6 × biology score). (d) Joint comparison of batch-removal and biological-preservation scores, highlighting limma as the most balanced method.