Figure 3

Illustrating the failure to map bead-centres correctly in the red channel. Illustrated are a small section of both the green (A) and red (B) images (with a slight shift to ensure alignment of the chip) from array section 4127130020_A_4. Nineteen beads are identified in the figure, and can be seen to follow a regular hexagonal lattice in the green image. The bead-centres for those nineteen beads (as provided by Illumina's software) are also plotted on the red image, where it is clear that there has been a failure in centre identification and mapping for some beads. Part C of the figure shows, for the nineteen beads, how far from the median value for the other replicates of these bead-types the reported log-intensity lies. Beads that are apparently not mapping to the correct bead in the red channel (B) are coloured red.