Effects of filtering by Present call on analysis of microarray experiments.

[Note that the signal and RMA values that remove similar numbers of probe sets are quite different for the vitamin A data than for the IFN data.] Increasing the stringency of filtering decreases the number of probe sets with nominally significant p-values, as expected, but the more significant probe sets (p ≤ 0.01 and p ≤ 0.001) are the least affected (Fig. 4 , Table 2 ).

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Requiring 100% Present in one of the two treatment groups is not recommended, because it removes too many highly significant probe sets (Tables 2 and 5 ) and removes a large portion of the probe sets turned on or off (Table 4 ) in experiments of any size.

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