Comparisons of distance methods for combining covariates and abundances in microbiome studies - PubMed (original) (raw)

Comparative Study

Comparisons of distance methods for combining covariates and abundances in microbiome studies

Julia Fukuyama et al. Pac Symp Biocomput. 2012.

Abstract

This article compares different methods for combining abundance data, phylogenetic trees and clinical covariates in a nonparametric setting. In particular we study the output from the principal coordinates analysis on UNIFRAC and WEIGHTED UNIFRAC distances and the output from a double principal coordinate analyses DPCOA using distances computed on the phylogenetic tree. We also present power comparisons for some of the standard tests of phylogenetic signal between different types of samples. These methods are compared both on simulated and real data sets. Our study shows that DPCoA is less robust to outliers, and more robust to small noisy fluctuations around zero.

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Figures

Fig. 1

Fig. 1

(a) shows ordination of community points by PCoA with the UniFrac metric; (b) by DPCoA. (c) shows ordination of species points by DPCoA: blue indicates species whose levels change in subjects A/B versus C/D, red indicates species whose levels change along a gradient related to location, and green indicates all other species.

Fig. 2

Fig. 2

Comparisons of DPCoA (row 1) and PCoA/MDS with unweighted UniFrac (row 2) for different noise levels. Columns correspond to data sets with noise levels .01, .2, and .39.

Fig. 3

Fig. 3

Comparing the UniFrac variants. From left to right: PCoA/MDS with unweighted UniFrac, with weighted UniFrac, and with weighted UniFrac performed on presence/absence data extracted from the abundance data used in the other two plots.

Fig. 4

Fig. 4

(a) PCoA/MDS of the

otus

based on the patristic distance, (b) community and (c) species points for DPCoA after removing two outlying species.

Fig. 5

Fig. 5

Community points as represented by DPCoA (left) and PCoA/MDS with unweighted UniFrac (right). The labels represent subject plus antibiotic condition. The ordinations are the same as in figures 4 and 3.

Fig. 6

Fig. 6

The left shows the _p_-values of the Mantel (circles), RV (pluses), and adonis (diamonds) tests for a location effect at different magnitudes of the effect. The right shows the _p_-values of the Abouheif (x's), adonis (diamonds), and UniFrac (triangles) tests at different magnitudes of the group effect.

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