Accéder directement au contenu Accéder directement à la navigation
Article dans une revue

Incorporating Phylogenetic Information in Microbiome Differential Abundance Studies Has No Effect on Detection Power and FDR Control

Abstract : We consider the problem of incorporating evolutionary information (e.g., taxonomic or phylogenic trees) in the context of metagenomics differential analysis. Recent results published in the literature propose different ways to leverage the tree structure to increase the detection rate of differentially abundant taxa. Here, we propose instead to use a different hierarchical structure, in the form of a correlation-based tree, as it may capture the structure of the data better than the phylogeny. We first show that the correlation tree and the phylogeny are significantly different before turning to the impact of tree choice on detection rates. Using synthetic data, we show that the tree does have an impact: smoothing p-values according to the phylogeny leads to equal or inferior rates as smoothing according to the correlation tree. However, both trees are outperformed by the classical, non-hierarchical, Benjamini-Hochberg (BH) procedure in terms of detection rates. Other procedures may use the hierarchical structure with profit but do not control the False Discovery Rate (FDR) a priori and remain inferior to a classical Benjamini-Hochberg procedure with the same nominal FDR. On real datasets, no hierarchical procedure had significantly higher detection rate that BH. Intuition advocates that the use of hierarchical structures should increase the detection rate of differentially abundant taxa in microbiome studies. However, our results suggest that current hierarchical procedures are still inferior to standard methods and more effective procedures remain to be invented.
Liste complète des métadonnées

Littérature citée [55 références]  Voir  Masquer  Télécharger

https://hal.inrae.fr/hal-02635268
Déposant : Mahendra Mariadassou <>
Soumis le : mercredi 27 mai 2020 - 17:35:14
Dernière modification le : mardi 17 novembre 2020 - 03:30:22

Licence


Distributed under a Creative Commons Paternité 4.0 International License

Identifiants

Collections

Citation

Antoine Bichat, Jonathan Plassais, Christophe Ambroise, Mahendra Mariadassou. Incorporating Phylogenetic Information in Microbiome Differential Abundance Studies Has No Effect on Detection Power and FDR Control. Frontiers in Microbiology, Frontiers Media, 2020, 11, ⟨10.3389/fmicb.2020.00649⟩. ⟨hal-02635268⟩

Partager

Métriques

Consultations de la notice

38

Téléchargements de fichiers

49