Quality Control and Low-Level Statistical Analysis of Illumina BeadArray

Abstract

The Illumina BeadArrayTM 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 BeadArrayTM data and high profile studies already being carried out using the BeadArrayTM technology, there is likely to be an increase in the volume of BeadArrayTM data available. A major advantage of BeadArrayTM 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 BeadArrayTM 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.

Keywords

• Illumina
• BeadArray
• beadarray
• Bioconductor
• microarray