Author:
Chen Athena,Kammers Kai,Larman H Benjamin,Scharpf Robert B.,Ruczinski Ingo
Abstract
AbstractPhage ImmunoPrecipitation Sequencing (PhIP-Seq) is a recently developed technology to assess antibody reactivity, quantifying antibody binding towards hundreds of thousands of candidate epitopes. The output from PhIP-Seq experiments are read count matrices, similar to RNA-Seq data; however some important differences do exist. In this manuscript we investigated whether the publicly available method edgeR (Robinson et al., Bioinformatics 26(1):139–140, 2010) for normalization and analysis of RNA-Seq data is also suitable for PhIP-Seq data. We find that edgeR is remarkably effective, but improvements can be made and introduce a Bayesian framework specifically tailored for data from PhIP-Seq experiments (Bayesian Enrichment Estimation in R, BEER).
Funder
National Institute of General Medical Sciences
National Institute of Allergy and Infectious Diseases
National Cancer Institute
Publisher
Springer Science and Business Media LLC
Cited by
3 articles.
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