Filtering based on the fraction of Present calls is superior to methods based on signal or RMA value because it is more likely to preserve probe sets turned on or off and it removes probe sets that show cross-hybridization. Filtering by fraction Present is also much easier to implement, because general guidelines can be set based upon the experiment size instead of having to examine the distribution of signal values; the variability of the signal distributions for different datasets is such that no average signal value gives comparable results across all datasets (Table 1). Although the detection call is generated by MAS5, this method can be used as a pre-filter to improve results using non-MAS5 generated data, such as RMA.
