Journal article
Statistical analysis in metabolic phenotyping
Nature Protocols
2021
Abstract
Metabolic phenotyping is an important tool in translational biomedical research. The advanced analytical technologies commonly used for phenotyping, including mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy, generate complex data requiring tailored statistical analysis methods. Detailed protocols have been published for data acquisition by liquid NMR, solid-state NMR, ultra-performance liquid chromatography (LC-)MS and gas chromatography (GC-)MS on biofluids or tissues and their preprocessing. Here we propose an efficient protocol (guidelines and software) for statistical analysis of metabolic data generated by these methods. Code for all steps is provided, and no prior coding skill is necessary. We offer efficient solutions for the different steps required within the complete phenotyping data analytics workflow: scaling, normalization, outlier detection, multivariate analysis to explore and model study-related effects, selection of candidate biomarkers, validation, multiple testing correction and performance evaluation of statistical models. We also provide a statistical power calculation algorithm and safeguards to ensure robust and meaningful experimental designs that deliver reliable results. We exemplify the protocol with a two-group classification study and data from an epidemiological cohort; however, the protocol can be easily modified to cover a wider range of experimental designs or incorporate different modeling approaches. This protocol describes a minimal set of analyses needed to rigorously investigate typical datasets encountered in metabolic phenotyping.
Details
- Title
- Statistical analysis in metabolic phenotyping
- Authors/Creators
- B.J. Blaise (Author/Creator) - King's College LondonG.D.S. Correia (Author/Creator) - Imperial College LondonG.A. Haggart (Author/Creator) - Imperial College LondonI. Surowiec (Author/Creator) - Sartorius AGC. Sands (Author/Creator) - Imperial College LondonM.R. Lewis (Author/Creator) - Imperial College LondonJ.T.M. Pearce (Author/Creator) - Imperial College LondonJ. Trygg (Author/Creator) - Sartorius AGJ.K. Nicholson (Author/Creator) - Murdoch UniversityE. Holmes (Author/Creator) - Murdoch UniversityT.M.D. Ebbels (Author/Creator) - Imperial College London
- Publication Details
- Nature Protocols
- Publisher
- Springer Nature
- Identifiers
- 991005544923207891
- Copyright
- © 2021 Springer Nature Limited
- Murdoch Affiliation
- Health Futures Institute; Australian National Phenome Centre
- Language
- English
- Resource Type
- Journal article
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- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 2 Chemistry
- 2.211 Mass Spectrometry
- 2.211.990 Metabolomics
- Web Of Science research areas
- Biochemical Research Methods
- ESI research areas
- Biology & Biochemistry