Batch correction for large-scale mass spectrometry imaging experiments
Abstract
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.
Fields of Study & Subjects
Mass Spectrometry Techniques and Applications
Advanced Proteomics Techniques and Applications
Metabolomics and Mass Spectrometry Studies
Publication details
- Journal / source
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Volume
- 42
- Issue
- 6
- Publication date
- 1 June 2026
- Language
- EN