Considerations for the processing and analysis of GoldenGate-based two-colour Illumina platforms

Illumina's GoldenGate technology is a two-channel microarray platform that allows for the simultaneous interrogation of about 1 500 locations in the genome. GoldenGate has proved a flexible platform not only in the choice of those 1 500 locations, but also in the choice of the property being measured at them. It retains the desirable properties of Illumina's BeadArrays in that the probes (in this case 'beads') are randomly arranged across the microarray, there are multiple instances of each probe and many samples can be processed simultaneously. As for other Illumina technologies, however, these properties are not exploited as they might be. Here we review the various common adaptations of the GoldenGate platform, review the analysis methods that are associated with each adaptation and then, with the aid of a number of example data sets we illustrate some of the improvements that can be made over the default analysis.