Spot analysis and quality control was automated using BlueFuse version 3.2 (BlueGnome, Cambridge, UK). Spots were excluded with quality flag < 1 or confidence value < 0.85. Triplicates of the spot ratios (Cy3/Cy5 intensity signals) were fused within BlueFuse in a confidence weighted fashion. The resulting log2 transformed ratios were normalized to their mode value.
confidence estimate of the AMPCH1/AMPCH2 ratio as calculated by BlueFuse, between 0 and 1
QUALITY
A quality flag determined as binary by BlueFuse to differentiate inferior spot quality (0) from sufficient spot quality (1)
VALUE
Mode normalized value of the log2 transformed AMPCH1/AMPCH2 ratio after fusion of replicates by BlueFuse, after exclusion of spots with confidence < 0.85 or quality < 1
