Batch correction for large-scale mass spectrometry imaging experiments

SUMMARY: We assess batch correction methods for MALDI mass spectrometry imaging experiments. ComBAT reduced batch-related technical variance, maintained biological variation, and improved the overall score by 19.4%. AVAILABILITY AND IMPLEMENTATION: Methods are available in R. comBAT is used through the "sva" package while Harmony, CCA, FastMNN are available in the "Seurat" package https://github.com/satijalab/seurat. scVI, scANVI are Scanorama are available in the Python programming language and through their github https://github.com/scverse/scvi-tools. Associated R code is found at DOI: https://doi.org/10.5281/zenodo.19730022.