The most pronounced difference between filtering by fraction Present and by average signal is the effect on probe sets that are turned "on" or "off". Genes that are turned on or off are of particular biological interest. In the IFN data there are 108 probe sets that met our criteria for being turned on or off (Table 4); there are 31 in the vitamin A data. Filtering by fraction Present, none of these probe sets were removed when the threshold was ≤ 50% for either data set. Filtering by signal value, on the other hand, removed "on/off" probe sets at each of the selected thresholds (Table 4). Demanding that all probe sets be Present in one of the two conditions leads to a 70% decrease in the detection of probe sets turned on or off in IFN data and an approximately 50% decrease for the vitamin A data.
