Comparison of RNA-seq and microarrays for the measurement of gene expression. Correlation between normalised hybridisation intensity and normalized read counts (RPKM) at a 50 M read depth for genes measureable using microarrays and RNA-Seq. A) Average expression for all three SNT samples. B) Average expression for all three naive samples. The red points show genes for which some expression level is measured by both platforms, blue points show genes that are not detected by RNA-seq (i.e. 0 reads aligned to the exons for that gene). Lines show the median (normalised) intensity for the antigenomic control probesets (solid line) and median + 1 median absolute deviation (dashed line). Some noise has been added to the expression values of these genes for clearer visualization of the point density.