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Data transformation, normalization and handling of batch effect are a keypart of data analysis for almost all spectrometry-based omics data. This paperreviews and contrasts these three distinct aspects. We present a systematicoverview of the key approaches and critically review some common procedures.Much of this paper is inspired by mass spectrometry based experimentation, butmost of our discussion carries over to omics data using distinct spectrometricapproaches generally.

Transformation, normalization and batch effect in the analysis of mass spectrometry data for omics studies