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Statistical Tools for Data Analysis

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Hydrocarbon and Lipid Microbiology Protocols

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Abstract

Microbial communities are complex and so are the data we use to describe them. In this chapter, we analyze a 16S amplicon data set from a marine time series using the open source QIIME software package. We first summarize complex, multivariate community composition data using ordination techniques. We then use the insights gained from ordination and multivariate statistical techniques to characterize the dominant relationships between environmental parameters and the microbial community in this marine ecosystem. Finally, we identify a list of taxa that show significant changes in relative abundance across seasons and describe the relationship between seasonality and community diversity. We go over several data visualization techniques that allow us to interpret our results. Analysis notes, QIIME commands, and sample data are provided. Finally, we discuss caveats regarding correlations and relative abundance data and describe how the statistical tools used in our 16S amplicon example can be applied to other types of “omics” data sets.

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Author information

Authors and Affiliations

  1. Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, USA

    Sean M. Gibbons

  2. Institute for Genomics and Systems Biology, Argonne National Laboratory, Chicago, IL, USA

    Sean M. Gibbons

Authors
  1. Sean M. Gibbons
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Corresponding author

Correspondence to Sean M. Gibbons .

Editor information

Editors and Affiliations

  1. Dept. Biological Sciences, University of Essex Dept. Biological Sciences, Colchester, Essex, United Kingdom

    Terry J. McGenity

  2. Braunschweig, Germany

    Kenneth N. Timmis

  3. University of the Balearic Islands , Palma de Mallorca, Spain

    Balbina Nogales Fernández

Coding Resources

Coding Resources

  1. 1.

    http://www.codecademy.com/

  2. 2.

    http://rosalind.info/problems/locations/

  3. 3.

    http://learnpythonthehardway.org/book/index.html

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© 2015 Springer-Verlag Berlin Heidelberg

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Gibbons, S.M. (2015). Statistical Tools for Data Analysis. In: McGenity, T., Timmis, K., Nogales Fernández, B. (eds) Hydrocarbon and Lipid Microbiology Protocols. Springer Protocols Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/8623_2015_50

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  • DOI: https://doi.org/10.1007/8623_2015_50

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-662-49309-0

  • Online ISBN: 978-3-662-49310-6

  • eBook Packages: Springer Protocols

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