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Activity Number: 352
Type: Contributed
Date/Time: Tuesday, August 2, 2016 : 10:30 AM to 12:20 PM
Sponsor: Biometrics Section
Abstract #319079 View Presentation
Title: Improved Phylogenetic Ordinations for Microbiome Data
Author(s): Julia Fukuyama*
Companies: Stanford University
Keywords: microbiome ; phylogenetic tree ; generalized PCA ; structured ordination ; empirical Bayes

A common step in the analysis of microbiome data is to visualize the samples using multi-dimensional scaling in combination with a phylogenetic tree-based distance such as weighted Unifrac. However, this method weights the deep branches of the tree very heavily, to the extent that true tree-related variation present in the data is often suppressed in a weighted Unifrac ordination. I give a mathematical explanation for this overweighting of the deep branches and present a new method that automatically decides how much weight to give to the deep branches compared to shallower branches. This method is based on a new interpretation of generalized PCA and can be used to make any kind of structured ordination (e.g. pathway-based ordination of gene expression or metabolite levels) in addition to phylogenetically structured ordinations. I illustrate the method on both simulated data and a real microbiome data set.

Authors who are presenting talks have a * after their name.

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