Constraining PERMANOVA and LDM to within-set comparisons by projection improves the efficiency of analyses of matched sets of microbiome data.

Microbiome
Zhengyi ZhuYi-Juan Hu

Abstract

Matched-set data arise frequently in microbiome studies. For example, we may collect pre- and post-treatment samples from a set of individuals, or use important confounding variables to match data from case participants to one or more control participants. Thus, there is a need for statistical methods for data comprised of matched sets, to test hypotheses against traits of interest (e.g., clinical outcomes or environmental factors) at the community level and/or the operational taxonomic unit (OTU) level. Optimally, these methods should accommodate complex data such as those with unequal sample sizes across sets, confounders varying within sets, and continuous traits of interest. PERMANOVA is a commonly used distance-based method for testing hypotheses at the community level. We have also developed the linear decomposition model (LDM) that unifies the community-level and OTU-level tests into one framework. Here we present a new strategy that can be used with both PERMANOVA and the LDM for analyzing matched-set data. We propose to include an indicator variable for each set as covariates, so as to constrain comparisons between samples within a set, and also permute traits within each set, which can account for exchangeable sample ...Continue Reading

References

Dec 29, 2010·PloS One·Emily S CharlsonRonald G Collman
Aug 13, 2014·Proceedings of the National Academy of Sciences of the United States of America·Patricio S La RosaPhillip I Tarr
Dec 18, 2014·Genome Biology·Michael I LoveSimon Anders
Jun 24, 2017·Menopause : the Journal of the North American Menopause Society·Caroline M MitchellDavid N Fredricks
Oct 21, 2017·Scientific Reports·Nicholas M VogtFederico E Rey
Dec 7, 2018·MSystems·Nicholas A BokulichJ Gregory Caporaso
Apr 9, 2019·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Tam T T TranDavid Vauzour

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Software Mentioned

R package ldm
MsFLASH
DESeq2
adonis2
permanovaFL
PERMANOVA
R package vegan

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