title: Generalized empirical Bayesian methods for discovery of differential data in high-throughput biology.
abstract: BACKGROUND
  High-throughput data are now commonplace in biological research. Rapidly changing technologies and application mean that novel methods for detecting differential behaviour that account for a 'large P, small n' setting are required at an increasing rate. The development of such methods is, in general, being done on an ad hoc basis, requiring further development cycles and a lack of standardization between analyses.
  
  
  RESULTS
  We present here a generalized method for identifying differential behaviour within high-throughput biological data through empirical Bayesian methods. This approach is based on our baySeq algorithm for identification of differential expression in RNA-seq data based on a negative binomial distribution, and in paired data based on a beta-binomial distribution. Here we show how the same empirical Bayesian approach can be applied to any parametric distribution, removing the need for lengthy development of novel methods for differently distributed data. Comparisons with existing methods developed to address specific problems in high-throughput biological data show that these generic methods can achieve equivalent or better performance. A number of enhancements to the basic algorithm are also presented to increase flexibility and reduce computational costs.
  
  
  METHODS
  The methods are implemented in the R baySeq (v2) package, available on Bioconductor http://www.bioconductor.org/packages/release/bioc/html/baySeq.html.
  
  
  BACKGROUND
  tjh48@cam.ac.uk
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK.
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Hardcastle
mesh_terms: D000465:Algorithms; D000818:Animals; D001499:Bayes Theorem; D016010:Binomial Distribution; D020869:Gene Expression Profiling / Q000379:methods*; D051381:Rats; D017423:Sequence Analysis, RNA; D012984:Software