Differential abundance analysis for microbial marker-gene surveys

doi:10.1038/NMETH.2658

Open AccessJournal ArticleDOI

Differential abundance analysis for microbial marker-gene surveys

Joseph N. Paulson, +3 more

- 01 Dec 2013 -

Nature Methods

- Vol. 10, Iss: 12, pp 1200-1202

TLDR

It is shown that metagenomeSeq outperforms the tools currently used in this field and relies on a novel normalization technique and a statistical model that accounts for undersampling in large-scale marker-gene studies.

Abstract:

We introduce a methodology to assess differential abundance in sparse high-throughput microbial 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 undersampling-a common feature of large-scale marker-gene studies. Using simulated data and several published microbiota data sets, we show that metagenomeSeq outperforms the tools currently used in this field.

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