Batch effects correction for microbiome data with Dirichlet-multinomial regression

doi:10.1093/bioinformatics/bty729

Batch effects correction for microbiome data with Dirichlet-multinomial regression

2018-08-23

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DOI：10.1093/bioinformatics/bty729

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Abstract Motivation Metagenomic sequencing techniques enable quantitative analyses of the microbiome. However, combining the microbial data from these experiments is challenging due to the variations between experiments. The existing methods for correcting batch effects do not consider the interactions between variables—microbial taxa in microbial studies—and the overdispersion of the microbiome data. Therefore, they are not applicable to microbiome data. Results We develop a new method, Bayesian Dirichlet-multinomial regression meta-analysis (BDMMA), to simultaneously model the batch effects and detect the microbial taxa associated with phenotypes. BDMMA automatically models the dependence among microbial taxa and is robust to the high dimensionality of the microbiome and their association sparsity. Simulation studies and real data analysis show that BDMMA can successfully adjust batch effects and substantially reduce false discoveries in microbial meta-analyses. Availability and implementation An R package” BDMMA” for Windows and Linux is available at https://github.com/DAIZHENWEI/BDMMA/BDMMA, and a version for MacOS is provided at https://github.com/DAIZHENWEI/BDMMA/BDMMA_MacOS. Supplementary information Supplementary data are available at Bioinformatics online.

Batch effects correction for microbiome data with Dirichlet-multinomial regression

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