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Microbiome Analysis pp 143–168Cite as

Normalization of Microbiome Profiling Data

Part of the Methods in Molecular Biology book series (MIMB,volume 1849)

Abstract

Normalization is a term that is often used but rarely defined and poorly understood. The number of choices of normalization procedure is large—some are inappropriate or inadmissible—and all are narrowly relevant to a specific analysis that depends on both the nature of the data and the question being asked. This chapter describes key definitions of normalization as they apply in metagenomics, mainly for taxonomic profiling data; while also demonstrating specific, reproducible examples of normalization procedures in the context of analysis techniques for which they were intended. The analysis and graphics code is distributed as a supplemental companion to this chapter so that the motivated reader can re-use it on new data.

Key words

  • Normalization
  • Microbiome
  • Metagenomics
  • DNA sequencing
  • Statistics

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Author information

Authors and Affiliations

  1. Whole Biome, Inc., San Francisco, CA, USA

    Paul J. McMurdie

Authors
  1. Paul J. McMurdie
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Correspondence to Paul J. McMurdie .

Editor information

Editors and Affiliations

  1. Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada

    Robert G. Beiko

  2. Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada

    Will Hsiao

  3. Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada

    Prof. Dr. John Parkinson

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McMurdie, P.J. (2018). Normalization of Microbiome Profiling Data. In: Beiko, R., Hsiao, W., Parkinson, J. (eds) Microbiome Analysis. Methods in Molecular Biology, vol 1849. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8728-3_10

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  • DOI: https://doi.org/10.1007/978-1-4939-8728-3_10

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  • Publisher Name: Humana Press, New York, NY

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  • Online ISBN: 978-1-4939-8728-3

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