Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes

ABSTRACT Differential abundance testing is a critical task in microbiome studies that is complicated by the sparsity of data matrices. Here we adapt for microbiome studies a solution from the field of gene expression analysis to produce a new method, discrete false-discovery rate (DS-FDR), that grea...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Lingjing Jiang, Amnon Amir, James T. Morton, Ruth Heller, Ery Arias-Castro, Rob Knight
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	differential abundance discrete test statistics FDR high dimension microbiome multiple comparison Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/b20aa14515844389a3aa08c36e38e634
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:b20aa14515844389a3aa08c36e38e634
record_format	dspace
spelling	oai:doaj.org-article:b20aa14515844389a3aa08c36e38e6342021-12-02T18:39:33ZDiscrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes10.1128/mSystems.00092-172379-5077https://doaj.org/article/b20aa14515844389a3aa08c36e38e6342017-12-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00092-17https://doaj.org/toc/2379-5077ABSTRACT Differential abundance testing is a critical task in microbiome studies that is complicated by the sparsity of data matrices. Here we adapt for microbiome studies a solution from the field of gene expression analysis to produce a new method, discrete false-discovery rate (DS-FDR), that greatly improves the power to detect differential taxa by exploiting the discreteness of the data. Additionally, DS-FDR is relatively robust to the number of noninformative features, and thus removes the problem of filtering taxonomy tables by an arbitrary abundance threshold. We show by using a combination of simulations and reanalysis of nine real-world microbiome data sets that this new method outperforms existing methods at the differential abundance testing task, producing a false-discovery rate that is up to threefold more accurate, and halves the number of samples required to find a given difference (thus increasing the efficiency of microbiome experiments considerably). We therefore expect DS-FDR to be widely applied in microbiome studies. IMPORTANCE DS-FDR can achieve higher statistical power to detect significant findings in sparse and noisy microbiome data compared to the commonly used Benjamini-Hochberg procedure and other FDR-controlling procedures.Lingjing JiangAmnon AmirJames T. MortonRuth HellerEry Arias-CastroRob KnightAmerican Society for Microbiologyarticledifferential abundancediscrete test statisticsFDRhigh dimensionmicrobiomemultiple comparisonMicrobiologyQR1-502ENmSystems, Vol 2, Iss 6 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	differential abundance discrete test statistics FDR high dimension microbiome multiple comparison Microbiology QR1-502
spellingShingle	differential abundance discrete test statistics FDR high dimension microbiome multiple comparison Microbiology QR1-502 Lingjing Jiang Amnon Amir James T. Morton Ruth Heller Ery Arias-Castro Rob Knight Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes
description	ABSTRACT Differential abundance testing is a critical task in microbiome studies that is complicated by the sparsity of data matrices. Here we adapt for microbiome studies a solution from the field of gene expression analysis to produce a new method, discrete false-discovery rate (DS-FDR), that greatly improves the power to detect differential taxa by exploiting the discreteness of the data. Additionally, DS-FDR is relatively robust to the number of noninformative features, and thus removes the problem of filtering taxonomy tables by an arbitrary abundance threshold. We show by using a combination of simulations and reanalysis of nine real-world microbiome data sets that this new method outperforms existing methods at the differential abundance testing task, producing a false-discovery rate that is up to threefold more accurate, and halves the number of samples required to find a given difference (thus increasing the efficiency of microbiome experiments considerably). We therefore expect DS-FDR to be widely applied in microbiome studies. IMPORTANCE DS-FDR can achieve higher statistical power to detect significant findings in sparse and noisy microbiome data compared to the commonly used Benjamini-Hochberg procedure and other FDR-controlling procedures.
format	article
author	Lingjing Jiang Amnon Amir James T. Morton Ruth Heller Ery Arias-Castro Rob Knight
author_facet	Lingjing Jiang Amnon Amir James T. Morton Ruth Heller Ery Arias-Castro Rob Knight
author_sort	Lingjing Jiang
title	Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes
title_short	Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes
title_full	Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes
title_fullStr	Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes
title_full_unstemmed	Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes
title_sort	discrete false-discovery rate improves identification of differentially abundant microbes
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/b20aa14515844389a3aa08c36e38e634
work_keys_str_mv	AT lingjingjiang discretefalsediscoveryrateimprovesidentificationofdifferentiallyabundantmicrobes AT amnonamir discretefalsediscoveryrateimprovesidentificationofdifferentiallyabundantmicrobes AT jamestmorton discretefalsediscoveryrateimprovesidentificationofdifferentiallyabundantmicrobes AT ruthheller discretefalsediscoveryrateimprovesidentificationofdifferentiallyabundantmicrobes AT eryariascastro discretefalsediscoveryrateimprovesidentificationofdifferentiallyabundantmicrobes AT robknight discretefalsediscoveryrateimprovesidentificationofdifferentiallyabundantmicrobes
_version_	1718377761270136832

Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes

Ejemplares similares