beadarray: R classes and methods for Illumina bead-based data
Bioinformatics, 2007•academic.oup.com
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 …
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 …
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: md392@cam.ac.uk
Oxford University Press