Correspondence between RNA-Seq and Exon arrays. (A) Determination of the read count threshold giving optimum correspondence between both platforms with respect to Present/Absent calls. (B) Present/Absent call correspondence at a read count threshold of zero in RNA-Seq and a DABG score threshold of 0.01 on the array. (C) Comparison of fold changes between RNA-Seq and the array. Red dots indicate exons flagged as Present (P) in both samples and on both platforms (PP->PP). Grey dots indicate exons flagged as Absent (A) in at least one sample on both platforms (AA->AA, PA->PA, AP->AP, PA-AP, AP->PA, AA->PA, AA->AP, PA->AA, AP->AA). Note that, due to the density of the data, some grey points representing exons Absent in both RNA-Seq samples (zero fold change) are masked by other colours. Blue dots indicate exons Absent in at least one RNA-Seq sample but flagged Present in both array samples (PA->PP, AA->PP, AP->PP), and green dots represent exons Present in both samples in RNA-Seq but flagged Absent in at least one sample on the array (PP->PA, PP->AA, PP->AP). (D) Overlap between numbers of exons called differentially expressed by the array and RNA-Seq using (Left) a log2 fold change threshold of 2.0 on the array and 3.0 in RNA-Seq (left) and a LIMMA p-value threshold of 1 × 10-4 on the array and an Audic-Claverie p-value threshold of 1 × 10-7 in RNA-Seq (right). These thresholds lead to the greatest equivalence between platforms using an overlap metric based on the CS (Equation 2).