Journal Article

R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips

Matthew E. Ritchie, Benilton S. Carvalho, Kurt N. Hetrick, Simon Tavaré and Rafael A. Irizarry

in Bioinformatics

Volume 25, issue 19, pages 2621-2623
Published in print October 2009 | ISSN: 1367-4803
Published online August 2009 | e-ISSN: 1460-2059 | DOI:

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Summary: Illumina produces a number of microarray-based technologies for human genotyping. An Infinium BeadChip is a two-color platform that types between 105 and 106 single nucleotide polymorphisms (SNPs) per sample. Despite being widely used, there is a shortage of open source software to process the raw intensities from this platform into genotype calls. To this end, we have developed the R/Bioconductor package crlmm for analyzing BeadChip data. After careful preprocessing, our software applies the CRLMM algorithm to produce genotype calls, confidence scores and other quality metrics at both the SNP and sample levels. We provide access to the raw summary-level intensity data, allowing users to develop their own methods for genotype calling or copy number analysis if they wish.

Availability and Implementation: The crlmm Bioconductor package is available from Data packages and documentation are available from


Journal Article.  1673 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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