Therefore it was provident to devise a strategy that allows two different transcripts to be identified by a single bead color. The 978 landmarks were divided into pairs and barcodes representing each gene were coupled to beads of the same color (one gene per bead). Genes coupled to the same bead type (color) in two separate batches were combined in a ratio of 2:1 prior to use. When the beads are hybridized with the sample templates and analyzed by the Luminex scanner, two values are obtained from each bead: one indicating the color of the bead and the other indicating the intensity of the signal, which is a reflection of the expression of the gene. Identification of the bead color associates the intensity to the correct gene pair and signal intensity provides a measure of the abundance of the transcripts of the two genes. Deconvolution of the composite fluorescent intensity signal into its component gene expression values is done computationally as described below. To make it easier to resolve the peaks, rather than pairing genes at random, during design of
