Batch correction for large-scale mass spectrometry imaging experiments
Abstract
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 implementationMethods 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 github: https://github.com/scverse/scvi-tools.
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