With the Illumina bead technology, a single hybridization of RNA from one cell line to an array produces on average approximately 30 intensity values for each of 47,294 bead types. These 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. In our experiment, each cell line was hybridized to two arrays, thus resulting in two reported intensity values (as averages of the values from the 30 beads per probe) for each of the 47,294 bead types. Hybridization intensity values were normalized on a log2 scale using a quantile normalization method [23] across replicates of a single individual followed by a median normalization method across all individuals of the eight populations. These normalized expression data for CEU, CHB, JPT, and YRI were used as input for the expression analysis, while the expression data from the populations with admixture (GIH, LWK, MEX, and MKK) were subjected to an additional correction for this genetic structure (See below).
