title: beadarray: R classes and methods for Illumina bead-based data.
abstract: The R/Bioconductor package beadarray allows raw data from Illumina experiments to be read and stored in convenient R classes. Users are free to choose between various methods of image processing, background correction and normalization in their analysis rather than using the defaults in Illumina's; proprietary software. The package also allows quality assessment to be carried out on the raw data. The data can then be summarized and stored in a format which can be used by other R/Bioconductor packages to perform downstream analyses. Summarized data processed by Illumina's; BeadStudio software can also be read and analysed in the same manner.
  
  
  BACKGROUND
  The beadarray package is available from the Bioconductor web page at www.bioconductor.org. A user's guide and example data sets are provided with the package.
authors.affiliation: Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK. md392@cam.ac.uk
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Dunning
authors.forename: Mike L
authors.initials: ML
authors.lastname: Smith
authors.forename: Matthew E
authors.initials: ME
authors.lastname: Ritchie
authors.forename: Simon
authors.initials: S
authors.lastname: Tavaré
mesh_terms: D000465:Algorithms; D030541:Databases, Genetic; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D008863:Microspheres; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011381:Programming Languages; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software