Figure 8.

Single-target: spike controls in single-target arrays Each panel shows the relation of spiked control probes (present for each dye-label) to other gene-probes on an array. Markers connected by lines indicate mean intensity level of genes on an array, corresponding markers not connected by lines indicate the mean of only the spiked control probes on the array. Spikes should be present at similar levels in all channels, although only one channel has been hybridised. As expected, spikes remain constant across all dye-labelled samples and blank channels. Normalisation constants based on the spike controls subset are small for all dye-label channels, and the variable hybridisation quality of the Cy3 arrays exceeds the adjustments that would be made by applying a subset normalisation. The consistency between the array replicates is still of sufficient degree to conclude that all single-target hybridisations result in small but measurable levels of signal for at least one of the two supposedly blank dye-label channels.