Correlations between actual TAR intensities and that predicted by nearest neighbor probes. TARs determined by tiling array data were tiled with virtual probes and assigned intensities using their nearest neighbors (see main text). Red points have an overall similarity score in the top fifth percentile (black list TARs; Additional file 2). Green points correspond to TARs having an overall similarity score in the bottom fifth percentile. Gray points are the rest. (a) Correlation between TAR intensities determined by the tiling array and the TAR intensities determined by using nearest neighbor probes. The intensities of TARs with high similarity to their nearest neighbor probes (red) are well correlated with the actual intensities (Spearman's correlation = 0.873). (b) Correlation between TAR intensities determined by RNA-Seq and the nearest neighbor "pseudoprobes." The correlation of highly similar TARs (red) is much lower (Spearman's correlation = 0.500).