Metabolomics Data Preprocessing: From Raw Data to Features for Statistical Analysis

Data preprocessing constitutes one of the most important stages in an untargeted metabolomics study. Every step of the workflow of data preparation from its 'raw' format to a table of metabolic features must be performed using clear and reproducible procedures to ensure that good datasets are produced. In this chapter, we will describe the general steps necessary to preprocess the complex datasets obtained in untargeted nuclear magnetic resonance spectroscopy and mass spectrometry-based metabolomics studies, from raw data to tables of features that can be used for statistical analysis.