Comparison of RNA-seq and microarrays for the detection of differentially expressed genes. A) Correlation between fold changes estimated by microarrays and RNA-seq (50 M read depth) for genes detectable by both technologies. There is an overall concordance in direction of fold change for the genes deemed as significantly DE by both platforms (red points), however a large number of DE genes are detected exclusively by RNA-seq (green points) or microarrays (blue points). B) Plot of the distributions of absolute log2 FCs for DE genes. FCs are shown for the genes that are called as DE by both platforms (red lines, dashed and solid lines show RNA-seq and microarray fold changes), using RNA-seq only (dashed green line) and microarrays only (solid blue line). Distribution curve computed using the probability density function, implemented in R. Ci-iii) Venn diagrams showing the number of genes found to be differentially expressed by RNA-seq at distinct read depths (Ci- 17 M; Cii- 25 M; Ciii-50 M) and the overlap with microarray data.