Boxplots of average absolute log (base 10) ratios between replicate arrays stratified by presence proportion for different statistical methods. (a) MBEI method; (b) AD method. The number of presence calls for a probe set in the 58 arrays for the six boxplots are: 0–9, 10–19, 20–29, 30–39, 40–49, 50–58. The title of each boxplot is the number of probe sets used for the boxplot. The average is taken over 29 replicate pairs. Log ratios are not calculated for negative expression values or expression values identified as 'array-outliers' by the MBEI method in either array of a replicate pair, and are not used to calculate the average. 744 probe sets are not included as their average absolute log ratios cannot be calculated for all the 29 pairs using either method.