Article

Differential abundance analysis for microbial marker-gene surveys

1] Graduate Program in Applied Mathematics & Statistics, and Scientific Computation, University of Maryland, College Park, Maryland, USA. [2] Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA.
Nature Methods (Impact Factor: 32.07). 09/2013; 10(12). DOI: 10.1038/nmeth.2658
Source: PubMed

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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Available from: Joseph Paulson, Feb 17, 2015
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    • "Alpha diversity (Shannon Index) was calculated on unfiltered data. Read counts were normalized using metagenomeSeq (Paulson et al., 2013) which utilizes a cumulative-sum scaling where raw counts are divided by the cumulative sum of counts up to a particular quantile. Principal Coordinate Analysis (PCoA) using Bray-Curtis dissimilarity indices, analysis of differential abundance of taxa, and beta diversity analysis using Whittaker's species turnover were performed on filtered and normalized data. "
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    • "Differential abundance analyses were conducted on the normalized OTU table using the 'fitZig' test in MetagenomeSeq on all OTUs with a variance threshold greater than 30 (Paulson et al., 2013). Results focus on classified clades (unless at the OTU level) with a relative abundance greater than 1% in at least one phase and all p-values were adjusted for multiple comparisons using the false discovery rate (Benjamini and Hochberg, 1995). "
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