Robust methods for differential abundance analysis in marker gene surveys

We introduce a novel methodology for differential abundance analysis in sparse high-throughput marker gene survey data. Our approach, implemented in the metagenomeSeq Bioconductor package, relies on a novel normalization technique and a statistical model that accounts for under-sampling: a common fe...

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Detalles Bibliográficos
Autores principales: Paulson, Joseph N., Stine, O. Colin, Bravo, Héctor Corrada, Pop, Mihai
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2013
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4010126/
https://www.ncbi.nlm.nih.gov/pubmed/24076764
http://dx.doi.org/10.1038/nmeth.2658
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author Paulson, Joseph N.
Stine, O. Colin
Bravo, Héctor Corrada
Pop, Mihai
author_facet Paulson, Joseph N.
Stine, O. Colin
Bravo, Héctor Corrada
Pop, Mihai
author_sort Paulson, Joseph N.
collection PubMed
description We introduce a novel methodology for differential abundance analysis in sparse high-throughput marker gene survey data. Our approach, implemented in the metagenomeSeq Bioconductor package, relies on a novel normalization technique and a statistical model that accounts for under-sampling: a common feature of large-scale marker gene studies. We show, using simulated data and several published microbiota datasets, that metagenomeSeq outperforms the tools currently used in this field.
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spelling pubmed-40101262014-06-01 Robust methods for differential abundance analysis in marker gene surveys Paulson, Joseph N. Stine, O. Colin Bravo, Héctor Corrada Pop, Mihai Nat Methods Article We introduce a novel methodology for differential abundance analysis in sparse high-throughput marker gene survey data. Our approach, implemented in the metagenomeSeq Bioconductor package, relies on a novel normalization technique and a statistical model that accounts for under-sampling: a common feature of large-scale marker gene studies. We show, using simulated data and several published microbiota datasets, that metagenomeSeq outperforms the tools currently used in this field. 2013-09-29 2013-12 /pmc/articles/PMC4010126/ /pubmed/24076764 http://dx.doi.org/10.1038/nmeth.2658 Text en Users may view, print, copy, download and text and data- mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Paulson, Joseph N.
Stine, O. Colin
Bravo, Héctor Corrada
Pop, Mihai
Robust methods for differential abundance analysis in marker gene surveys
title Robust methods for differential abundance analysis in marker gene surveys
title_full Robust methods for differential abundance analysis in marker gene surveys
title_fullStr Robust methods for differential abundance analysis in marker gene surveys
title_full_unstemmed Robust methods for differential abundance analysis in marker gene surveys
title_short Robust methods for differential abundance analysis in marker gene surveys
title_sort robust methods for differential abundance analysis in marker gene surveys
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4010126/
https://www.ncbi.nlm.nih.gov/pubmed/24076764
http://dx.doi.org/10.1038/nmeth.2658
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AT bravohectorcorrada robustmethodsfordifferentialabundanceanalysisinmarkergenesurveys
AT popmihai robustmethodsfordifferentialabundanceanalysisinmarkergenesurveys

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