ratio vs Signal Intensity scatter plots obtained by MAIA (A) and GP (B) for a selected control microarray. The fixed number of down-, invariant-, and up- features, found "good" by both programs, is selected for the statistical comparison. Procedures of girding and image quantifications were done automatically as recommended in the corresponding manuals of MAIA and GP. A control microarray consists of three populations of spots with expected Log2 ratios of -1.58 (3:1), 0 (1:1), and 1.58 (1:3) [see Additional file 2]. Data yielded by the GP analysis are more dispersive. We assume that no normalisation procedure is required for these data even at low signal intensities, where the experimental data may deviate from the theoretical values. Data are not calibrated and not normalized.