Introduction

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.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.The methods are implemented in the R baySeq (v2) package, available on Bioconductor http://www.bioconductor.org/packages/release/bioc/html/baySeq.html.tjh48@cam.ac.ukSupplementary data are available at Bioinformatics online.

Publications

  1. Generalized empirical Bayesian methods for discovery of differential data in high-throughput biology.
    Cite this
    Hardcastle TJ, 2016-01-01 - Bioinformatics (Oxford, England)

Credits

  1. Thomas J Hardcastle
    Investigator

    Department of Plant Sciences, University of Cambridge, United Kingdom of Great Britain and Northern Ireland

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Summary
AccessionBT001363
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Submitted ByThomas J Hardcastle