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A model for paired‐multinomial data and its application to analysis of data on a taxonomic tree

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  • Pixu Shi
  • Hongzhe Li

Abstract

In human microbiome studies, sequencing reads data are often summarized as counts of bacterial taxa at various taxonomic levels specified by a taxonomic tree. This article considers the problem of analyzing two repeated measurements of microbiome data from the same subjects. Such data are often collected to assess the change of microbial composition after certain treatment, or the difference in microbial compositions across body sites. Existing models for such count data are limited in modeling the covariance structure of the counts and in handling paired multinomial count data. A new probability distribution is proposed for paired‐multinomial count data, which allows flexible covariance structure and can be used to model repeatedly measured multivariate count data. Based on this distribution, a test statistic is developed for testing the difference in compositions based on paired multinomial count data. The proposed test can be applied to the count data observed on a taxonomic tree in order to test difference in microbiome compositions and to identify the subtrees with different subcompositions. Simulation results indicate that proposed test has correct type 1 errors and increased power compared to some commonly used methods. An analysis of an upper respiratory tract microbiome data set is used to illustrate the proposed methods.

Suggested Citation

  • Pixu Shi & Hongzhe Li, 2017. "A model for paired‐multinomial data and its application to analysis of data on a taxonomic tree," Biometrics, The International Biometric Society, vol. 73(4), pages 1266-1278, December.
    • Handle: RePEc:bla:biomet:v:73:y:2017:i:4:p:1266-1278
    DOI: 10.1111/biom.12681
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    1. Jeffrey R. Wilson, 1989. "Chi‐Square Tests for Overdispersion with Multiparameter Estimates," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 38(3), pages 441-453, November.
    2. Steven N. Evans & Frederick A. Matsen, 2012. "The phylogenetic Kantorovich–Rubinstein metric for environmental sequence samples," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 74(3), pages 569-592, June.
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