Spatial biases differ between the foreground and background. Images of Cy3 background (A), Cy5 background (B), Cy3 foreground (C) and Cy5 foreground (D) signal calls for a representative microarray. Shown are signals smoothed by an averaging filter to expose spatial trends. Spatial biases differ between the background and foreground as well as between the different dyes. The corresponding autocorrelation signal of the microarray shown can be seen in Figure 3C, lane 5.