beadarray: R classes and methods for Illumina bead-based data

Bioinformatics. 2007 Aug 15;23(16):2183-4. doi: 10.1093/bioinformatics/btm311. Epub 2007 Jun 22.


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.

Availability: The beadarray package is available from the Bioconductor web page at A user's guide and example data sets are provided with the package.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Databases, Genetic
  • Image Interpretation, Computer-Assisted / methods*
  • In Situ Hybridization, Fluorescence / methods*
  • Microspheres
  • Oligonucleotide Array Sequence Analysis / methods*
  • Programming Languages*
  • Sequence Analysis, DNA / methods*
  • Software*