Intensity and spatial distribution of raw log intensity ratios M of slide 3 of the SW480/620 experiment. (a) The MA-plot indicates a strong bias towards the Cy3 channel for low spot intensities A. (b) The spatial MXY-plot shows uneven distribution of positive M (red squares) and negative M (green squares). The columns with consistently negative M correspond to empty control spots. The axis labels X and Y refer to the spot location as determined by the QuantArray scanning software.