Scatter plots between hybridisations with bovine adult brain (A-C) and correlations within the whole design (D). Signal mean intensities were calculated for each amplified target on 4 arrays and plotted pair-wise per replicate. For example, PCR-amplified: replicate 1 versus replicate 2 (A) and IVT-amplified: replicate 1 versus replicate 2 (B). Similar results were obtained for the 4 other pairs (1 versus 3 and 2 versus 3). Signal mean intensities per protocol were calculated on 12 arrays (4 arrays per replicate × 3 replicates) and plotted pair-wise per protocol (C): PCR-amplified versus IVT-amplified. Similar results were obtained for the ovary and the embryos (ovoid, tubular and filamentous stages). Correlation factors between hybridisation profiles (D).