Background-corrected values for a single bead type are subsequently summarized by Illumina software and output to the user as a set of 47,294 intensity values for each individual hybridization 25. To combine data from our multiple replicate hybridizations, raw data were read using the beadarray R package 24 and then normalized on a log scale using a quantile normalization method 41 across replicates of a single individual, followed by a median normalization method across all 270 individuals.
