title: BeadArray expression analysis using bioconductor.
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.
authors.affiliation: Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. mritchie@wehi.edu.au
authors.forename: Matthew E
authors.initials: ME
authors.lastname: Ritchie
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Dunning
authors.forename: Mike L
authors.initials: ML
authors.lastname: Smith
authors.forename: Wei
authors.initials: W
authors.lastname: Shi
authors.forename: Andy G
authors.initials: AG
authors.lastname: Lynch
mesh_terms: D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012107:Research Design; D012984:Software