Benchmarking of bulk transcriptomic harmonization tools in a multi-platform B-cell lymphoma cohort identifies feature-specific quantile normalization and surrogate variable analysis as top-performing methods
Daniil M. Nikitin, Nikolay Borisov, Maria Savchenko, Anatoly S. Bobe, Mark Meerson, Alexander A. Nesmelov, Nazar Harutyunyan, Svetlana Paponova, Andrey Kravets, Alexandr Zaitsev, Alexander Bagaev, Arsen Arakelyan
Across 7,174 multi-platform lymphoma transcriptomes, only surrogate variable analysis and feature-specific quantile normalization corrected batch effects while keeping subtype and normal B-cell differences; top-scoring MNN erased biomarker correlations.
bioRxiv · Sep 17, 2026 · PreprintCancer Biology✦ In-depth digest