Quality Control and Low-Level Statistical Analysis of Illumina BeadArray

Abstract

The Illumina BeadArray^TM platform is a novel microarray technology based on randomly assembled arrays of beads. Each bead on the array carries copies of a single gene-specific probe with, on average, about 30 replicates of each bead type on an array. Given the encouraging results regarding the reproducibility of BeadArray^TM data and high profile studies already being carried out using the BeadArray^TM technology, there is likely to be an increase in the volume of BeadArray^TM data available. A major advantage of BeadArray^TM technology is the high degree of replication of beads of a given type. However, current analysis methods give summarised information for each bead type as output rather than information for each individual bead on the array. The beadarray R package is able to recreate individual bead information for arrays using raw images as input. Here, we use a particular experiment to illustrate the image processing steps used by Illumina and corresponding methods available in beadarray. Our investigations into BeadArray^TM data have demonstrated a high degree of reproducibility both within and between arrays. However, we identified some aspects of the low-level analysis that could be improved.