The first method used the fraction called Present in at least one treatment group to filter. For each probe set on each array, MAS5 provides a detection call, Absent (A), Present (P) or Marginal (M), which indicates whether the specific mRNA is detectable. The detection call in MAS5 is based on a non-parametric statistical test (Wilcoxon signed rank test) [5] of whether significantly more perfect matches show more hybridization signal than their corresponding mismatches. For each probe set, the number of Present and Marginal calls in each treatment group were summed using a value of 1 for Present and 0.51 for Marginal. Probe sets that met or exceeded a particular threshold of fraction Present in at least one treatment group were retained. For example using the IFN data, for a 50% fraction Present filter, probe sets were retained if the "number Present" was at least 5 in either treatment group for the 10 × 10 experiment; for 25% the number Present must be at least 2.5 in either treatment group. RMA does not provide a measure comparable to the MAS5 detection call, therefore we used the MAS5 detection call to filter the RMA data sets as well.
