Analysis of a data matrix and a graph: metagenomic data and the phylogenetic tree

DOI10.1214/10-AOAS402MaRDI QIDQ765971zbMATH OpenFDO

Authors Elizabeth Purdom

Publication date 22 March 2012

Published in The Annals of Applied Statistics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1202.5880

zbMATH Keywords

principal componentsmultivariate analysis

Mathematics Subject Classification ID

Factor analysis and principal components; correspondence analysis (62H25) Applications of statistics to biology and medical sciences; meta analysis (62P10) Problems related to evolution (92D15) Graph theory (05C99)

Abstract: In biological experiments researchers often have information in the form of a graph that supplements observed numerical data. Incorporating the knowledge contained in these graphs into an analysis of the numerical data is an important and nontrivial task. We look at the example of metagenomic data---data from a genomic survey of the abundance of different species of bacteria in a sample. Here, the graph of interest is a phylogenetic tree depicting the interspecies relationships among the bacteria species. We illustrate that analysis of the data in a nonstandard inner-product space effectively uses this additional graphical information and produces more meaningful results.

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Cited in

(7)

• Kernel-penalized regression for analysis of microbiome data
• The travelling salesman problem: selected algorithms and heuristics†
• The duality diagram in data analysis: examples of modern applications
• Principal component analysis for zero-inflated compositional data
• A statistical analysis of the towers of hanoi problem
• A statistical perspective on the challenges in molecular microbial biology
• Adaptive gPCA: a method for structured dimensionality reduction with applications to microbiome data

Describes a project that uses

Uses Software

• sedaR
• ade4
• R

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