hybridization ratio variation. Scatterplots showing the difference in hybridization signal between two independent arrays. Data points represent normalized signal intensities (log2 scale) of oligonucleotides. Colors indicate the number of data points that have been grouped for a better visualization (see color bar for scale). A) Intra strain variation of signal intensity. Two independent samples of PAO1 DNA were comparatively hybridized. Signal intensities show high correlation (R = 0.935) with most data points being close to the diagonal. B) Variation of signal intensity between PA14 and PAO1. Two single arrays were comparatively hybridized with PA14 DNA and PAO1 DNA, respectively. The large cloud of data points below the diagonal indicates sequence variations that lead to decreased signal ratios for the affected oligonucleotide probes. Data points significantly above the diagonal (arrows) are due to a 1 kb deletion in the reference PAO1 strain (for details see Figure 7 and text). Note that a small proportion (~2%) of signals shows saturation effects leading to the strict edges of the data clouds.