Quality control and low-level statistical analysis of Illumina BeadArrays The Illumina BeadArray 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 data and high profile studies already being carried out using the BeadArray technology, there is likely to be an increase in the volume of BeadArray data available. A major advantage of BeadArray 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 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.

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