Adaptive gPCA: a method for structured dimensionality reduction with applications to microbiome data

DOI10.1214/18-AOAS1227MaRDI QIDQ2318673zbMATH OpenWikidataFDO

Authors Julia Fukuyama

Publication date 15 August 2019

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

Full work available at URL https://projecteuclid.org/euclid.aoas/1560758437

zbMATH Keywords

adaptive generalized principal components analysisadaptive gPCAempirical BayesmicrobiomePCAphylogeny

Mathematics Subject Classification ID

Factor analysis and principal components; correspondence analysis (62H25) Applications of statistics to biology and medical sciences; meta analysis (62P10)

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Cites work

• A generalized least-square matrix decomposition
• A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis
• Adaptive gPCA: a method for structured dimensionality reduction with applications to microbiome data
• Analysis of a data matrix and a graph: metagenomic data and the phylogenetic tree
• DESeq2
• From dissimilarities among species to dissimilarities among communities: a double principal coordinate analysis
• scientific article; zbMATH DE number 3111121 (Why is no real title available?)
• Kernel-penalized regression for analysis of microbiome data
• Multivariate data analysis: The French way
• On consistency and sparsity for principal components analysis in high dimensions
• Properties and refinements of the fused Lasso
• Sparsity and Smoothness Via the Fused Lasso
• Spatial smoothing and hot spot detection for CGH data using the fused lasso

Cited in

(5)

• A statistical perspective on the challenges in molecular microbial biology
• Adaptive gPCA: a method for structured dimensionality reduction with applications to microbiome data
• Simultaneous dimension reduction and adjustment for confounding variation
• Poisson PCA: Poisson measurement error corrected PCA, with application to microbiome data
• Modelling phylogeny in 16s rRNA gene sequencing datasets using string-based kernels

Describes a project that uses

Uses Software

• DESeq2
• adaptiveGPCA
• Bioconductor
• R
• ape
• PMA

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