Schematic describing the tiling array analysis and FPR calibration pipeline. First, we optimize the threshold, maxgap, and minrun parameters of tiling arrays and RNA-Seq segmentation, notated T, G, and R, respectively. To do this, we compare the called TARs to a manually curated gold standard set and do a brute-force search over the parameter space to attain an FPR of 0.05 with maximum sensitivity. Then, as detailed in the main text, we calculate a rank score for each tiling array TAR by comparing its intensity to a distribution of null TARs constructed from non-exonic regions. We then map this value to a marginal FPR, which is calculated by sorting the TARs based on their rank score and then iteratively selecting smaller subsets of TARs, assigning the FPR to the TAR defining the outermost boundary. This marginal FPR can then be adjusted by following a similar procedure using the RNA-Seq data as a gold standard set, giving a calibrated marginal FPR for each TAR.