does not provide a measure comparable to the MAS5 detection call. We examined the effects of the fraction Present filtering on the ability to detect changes in expression using a parametric t-test and also using a permutation-based test, significance analysis of microarrays (SAM) [19]. We also explore how experiment size can affect the ability to detect differences in gene expression, and how the sample size interacts with the choice of filtering thresholds, using permutations of the full data set to create virtual experiments of smaller sample sizes. These analyses provide useful guidelines for improving the design and interpretation of microarray experiments.
