We compared the two methods when comparable numbers of probe sets were retained for analysis. To do this, for each of the selected fraction Present thresholds, we calculated the number of probe sets retained and set an average threshold for either MAS5 signal or RMA value that retained a comparable number of probe sets. For example, using the IFN data, 10,678 probe sets were retained after filtering by a fraction Present threshold of 50%; therefore we selected an average signal of 475 to retain 10,675 probe sets and an average RMA value of 5.03 to retain 10,687 probe sets for comparison.
