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Model-Based Background Correction (MBCB): R Methods and GUI for Illumina Bead-array Data

Abstract

Jeffrey D. Allen, Min Chen and Yang Xie

Summary: Illumina BeadArray platform (Illumina Inc.) is playing an increasing role in cancer research. MBCB, an R package designed for use on Illumina Bead-Array data, allows for microarray data to be pre-processed through various model-based statistical methods. These model-based background-correction methods have proven to be a significant improvement over the traditional methods provided by Illumina in their BeadStudio software. MBCB accepts the summarized bead-type data; the data can then be normalized and background-corrected in a statistically-efficient manner. When compared to the popular Robust multi-array (RMA) background correction approach and the default, Illuminaprovided background-correction method, MBCB has shown to lead to more precise determination of gene expression and better biological interpretation of Illumina BeadArray data. The software developed will facilitate molecular biomedical - especially cancer - research. Availability: This package will soon be available from Bioconductor. Instructions for use are included with the package.