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Bioinformatics Advance Access originally published online on February 4, 2009
Bioinformatics 2009 25(6):751-757; doi:10.1093/bioinformatics/btp040
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Statistical methods of background correction for Illumina BeadArray data

Yang Xie 1,2,*, Xinlei Wang 3 and Michael Story 2,4

1Division of Biostatistics, Department of Clinical Sciences, 2Simmons Cancer Center, University of Texas Southwestern Medical Center, 3Department of Statistical Science, Southern Methodist University and 4Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Advances in technology have made different microarray platforms available. Among the many, Illumina BeadArrays are relatively new and have captured significant market share. With BeadArray technology, high data quality is generated from low sample input at reduced cost. However, the analysis methods for Illumina BeadArrays are far behind those for Affymetrix oligonucleotide arrays, and so need to be improved.

Results: In this article, we consider the problem of background correction for BeadArray data. One distinct feature of BeadArrays is that for each array, the noise is controlled by over 1000 bead types conjugated with non-specific oligonucleotide sequences. We extend the robust multi-array analysis (RMA) background correction model to incorporate the information from negative control beads, and consider three commonly used approaches for parameter estimation, namely, non-parametric, maximum likelihood estimation (MLE) and Bayesian estimation. The proposed approaches, as well as the existing background correction methods, are compared through simulation studies and a data example. We find that the maximum likelihood and Bayes methods seem to be the most promising.

Contact: yang.xie{at}utsouthwestern.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: David Rocke

Received on September 26, 2008; revised on December 18, 2008; accepted on January 17, 2009

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