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Bioinformatics Advance Access published online on February 4, 2009
Bioinformatics, 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 a,b,*, Xinlei Wang c and Michael Story d,b

a Division of Biostatistics, Department of Clinical Sciences,University of Texas Southwestern Medical Center, Dallas, U.S.A
b Simmons Cancer Center,University of Texas Southwestern Medical Center , Dallas, U.S.A
c Department of Statistical Science, Southern Methodist University, Dallas, U.S.A
d Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas,

*to whom correspondence should be addressed. Dr. Yang Xie, E-mail: yang.xie{at}utsouthwestern.edu


  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 paper, 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 one thousand bead types conjugated with non-specific oligonucleotide sequences. We extend the RMA background correction model to incorporate the information from negative control beads, and consider three commonly used approaches for parameter estimation, namely, nonparametric, maximum likelihood 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

Associate Editor: Prof. David Rocke

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

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