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Public Library of Science, PLoS Computational Biology, 12(7), p. e1002276, 2011

DOI: 10.1371/journal.pcbi.1002276

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BeadArray Expression Analysis Using Bioconductor

Journal article published in 2011 by Matthew E. Ritchie, Mark J. Dunning ORCID, Mike L. Smith, Wei Shi, Andy G. Lynch
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Illumina whole-genome expression BeadArrays are a popular choice in gene profiling studies. Aside from the vendor-provided software tools for analyzing BeadArray expression data (GenomeStudio/BeadStudio), there exists a comprehensive set of open-source analysis tools in the Bioconductor project, many of which have been tailored to exploit the unique properties of this platform. In this article, we explore a number of these software packages and demonstrate how to perform a complete analysis of BeadArray data in various formats. The key steps of importing data, performing quality assessments, preprocessing, and annotation in the common setting of assessing differential expression in designed experiments will be covered.