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

TLDR

beadarray provides R classes for reading and storing Illumina bead‑based data, allowing users to apply diverse image processing, background correction, and normalization methods instead of Illumina’s defaults, and to assess data quality. It summarizes and stores the data in R classes that are compatible with other Bioconductor packages, and can also import and analyze data from Illumina’s BeadStudio. The beadarray package, along with a user guide, example data sets, and contact information, is available from the Bioconductor website (www.bioconductor.org).

Abstract

Abstract Summary: 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 www.bioconductor.org. A user's; guide and example data sets are provided with the package. Contact: [e-mail]