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Differential abundance analysis for microbial marker-gene surveys.

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.

SUBMITTER: Paulson JN 

PROVIDER: S-EPMC4010126 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature

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Differential abundance analysis for microbial marker-gene surveys.

Paulson Joseph N JN   Stine O Colin OC   Bravo Héctor Corrada HC   Pop Mihai M  

Nature methods 20130929 12

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. ...[more]