Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville Victoria 3052, Australia.
Bioinformatics. 2009 Oct 1;25(19):2621-3. doi: 10.1093/bioinformatics/btp470. Epub 2009 Aug 6.
Illumina produces a number of microarray-based technologies for human genotyping. An Infinium BeadChip is a two-color platform that types between 10(5) and 10(6) 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.
The crlmm Bioconductor package is available from http://www.bioconductor.org. Data packages and documentation are available from http://rafalab.jhsph.edu/software.html.
Illumina 生产了许多用于人类基因分型的基于微阵列的技术。Infinium BeadChip 是一种双色平台，每个样本可对 10(5)到 10(6)个单核苷酸多态性 (SNP) 进行分型。尽管它被广泛使用，但缺乏用于将该平台的原始强度数据处理成基因型调用的开源软件。为此，我们开发了用于分析 BeadChip 数据的 R/Bioconductor 包 crlmm。经过仔细的预处理，我们的软件应用 CRLMM 算法在 SNP 和样本水平上生成基因型调用、置信得分和其他质量指标。我们提供原始汇总级强度数据的访问权限，如果用户愿意，允许他们开发自己的基因型调用或拷贝数分析方法。
crlmm Bioconductor 包可从 http://www.bioconductor.org 获取。数据包和文档可从 http://rafalab.jhsph.edu/software.html 获取。
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