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Extracting Meaningful Information from Metabonomic Data Using Multivariate Statistics

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Metabonomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1277))

Abstract

Metabonomics aims to identify and quantify all small-molecule metabolites in biologically relevant samples using high-throughput techniques such as NMR and chromatography/mass spectrometry. This generates high-dimensional data sets with properties that require specialized approaches to data analysis. This chapter describes multivariate statistics and analysis tools to extract meaningful information from metabonomic data sets. The focus is on the use and interpretation of latent variable methods such as principal component analysis (PCA), partial least squares/projections to latent structures (PLS), and orthogonal PLS (OPLS). Descriptions of the key steps of the multivariate data analyses are provided with demonstrations from example data.

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References

  1. Johnson RA, Wichern DW (2002) Applied multivariate statistical analysis. Prentice-Hall, Upper Saddle River

    Google Scholar 

  2. Esbensen K, Guyot D, Westad F, Houmoller LP (2002) Multivariate data analysis-in practice: an introduction to multivariate data analysis and experimental design. CAMO, Oslo

    Google Scholar 

  3. Jolliffe IT (2002) Principal component analysis. Springer, New York

    Google Scholar 

  4. Wold S, Sjöström M, Eriksson L (2001) PLS-regression: a basic tool of chemometrics. Chemom Intell Lab Syst 58:109–130

    Article  CAS  Google Scholar 

  5. Trygg J, Wold S (2002) Orthogonal projections to latent structures (O‐PLS). J Chemom 16:119–128

    Article  CAS  Google Scholar 

  6. Bylesjö M, Rantalainen M, Cloarec O et al (2006) OPLS discriminant analysis: combining the strengths of PLS‐DA and SIMCA classification. J Chemom 20:341–351

    Article  Google Scholar 

  7. York B, Sagen JV, Tsimelzon A et al (2013) Research resource: tissue-and pathway-specific metabolomic profiles of the steroid receptor coactivator (SRC) family. Mol Endocrin 27:366–380

    Article  CAS  Google Scholar 

  8. Core Team R (2013) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna

    Google Scholar 

  9. Stacklies W, Redestig H, Scholz M et al (2007) pcaMethods – a bioconductor package providing PCA methods for incomplete data. Bioinformatics 23:1164–1167

    Article  CAS  PubMed  Google Scholar 

  10. Mevik BH, Wehrens R (2007) The pls package: principal component and partial least squares regression in R. J Stat Software 18:1–24

    Article  Google Scholar 

  11. Bylesjö M, Eriksson D, Sjödin A et al (2007) Orthogonal projections to latent structures as a strategy for microarray data normalization. BMC Bioinformatics 8:207

    Article  PubMed Central  PubMed  Google Scholar 

  12. Westerhuis JA, Hoefsloot HC, Smit S et al (2008) Assessment of PLSDA cross validation. Metabolomics 4:81–89

    Article  CAS  Google Scholar 

  13. Chagoyen M, Pazos F (2013) Tools for the functional interpretation of metabolomic experiments. Brief Bioinform 14:737–744

    Article  PubMed  Google Scholar 

  14. Krzanowski WJ (1987) Cross-validation in principal component analysis. Biometrics 43:575–584

    Article  Google Scholar 

  15. Cattell RB (1966) The scree test for the number of factors. Multivar Behav Res 1:245–276

    Article  Google Scholar 

  16. Cloarec O, Dumas ME, Craig A et al (2005) Statistical total correlation spectroscopy: an exploratory approach for latent biomarker identification from metabolic 1H NMR data sets. Anal Chem 77:1282–1289

    Article  CAS  PubMed  Google Scholar 

  17. Ramadan Z, Jacobs D, Grigorov M et al (2006) Metabolic profiling using principal component analysis, discriminant partial least squares, and genetic algorithms. Talanta 68:1683–1691

    Article  CAS  PubMed  Google Scholar 

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Correspondence to Max Bylesjö .

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Bylesjö, M. (2015). Extracting Meaningful Information from Metabonomic Data Using Multivariate Statistics. In: Bjerrum, J. (eds) Metabonomics. Methods in Molecular Biology, vol 1277. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2377-9_11

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  • DOI: https://doi.org/10.1007/978-1-4939-2377-9_11

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2376-2

  • Online ISBN: 978-1-4939-2377-9

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