Journal article

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

Matthew E Ritchie, Benilton S Carvalho, Kurt N Hetrick, Simon Tavare, Rafael A Irizarry

BIOINFORMATICS | OXFORD UNIV PRESS | Published : 2009

Abstract

UNLABELLED: 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, allow..

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University of Melbourne Researchers

Grants

Awarded by Isaac Newton Trust and NHMRC Program


Awarded by NHMRC IRIISS


Awarded by National Institutes of Health


Awarded by NATIONAL CENTER FOR RESEARCH RESOURCES


Awarded by NATIONAL HUMAN GENOME RESEARCH INSTITUTE


Awarded by NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES


Awarded by Cancer Research UK


Funding Acknowledgements

Isaac Newton Trust and NHMRC Program ( grant 406657); NHMRC IRIISS ( grant 361646); Victorian State Government OIS grant ( to M. E. R.); National Institutes of Health grants R01GM083084, R01RR021967 and P41HG004059 ( to B. S. C., R. A. I.); Cancer Research UK( S. T.). Funding for open access charge: National Institutes of Health ( grant P41HG004059).