Figure 4.

Intensity variance and covariance for microarray spots. (a) Plot of Cy3 vs. Cy5 signal on a pixel by pixel basis for the Spot A and Spot B of Fig. 3. Arrows denote the direction of covariance, in which intensities in the red and green rise and fall together, and of ratio variance (SRV), in which the channels rise and fall independently. (b) Relationship of covariance and intensity variance for 6,200 spots (blue dots and red trend-line). (Insets) Images of spots lying well away from the trend-line (indicated by red circles). To illustrate the effect of a misalignment of one or more pixels, a common problem with laser scanners, a single pixel shift was introduced into the original scan data (green dots, pink trend-line). The average correlation coefficient decreased from 0.85 to 0.41 (1.00 is the maximum possible) and the average SRV increased almost 3-fold. (c) Comparison of SRV values (blue dots) to a recently published parameterized error model (red line; ref. 12).