Correlation of microarray and real-time PCR measurements, stratified by location of probe for EDNRA and IFG1. The x-axis gives the position of a probe along the length of the gene. The y-axis gives the Pearson correlation between microarray probe set intensity and RPLP0-/TBP-normalized real-time PCR Ct value, both preprocessed as described in the methods section. Microarray probe sets are shown at a height corresponding to their correlation, with one dot for each probe in the set. Exact real-time PCR primer location is not available from Applied Biosystems, but the exon location of an assay is given. The locations of them are therefore marked with a thick horizontal line at a fixed height on the plot. The exon-intron architecture is indicated below the real-time PCR location. The value of the correlation is given in the first line below the plot. In some cases, the microarray probes were not found to match in the gene sequence used. They are likely to be probe sets for obsolete or alternative transcript isoforms. The correlation of these cases is indicated in the second line below the plot. The third line below the plot specifies how many real-time PCR double measurements had coefficients of variance above the threshold of 0.02. Additional file 4 contains this type of plot for all target genes. A figure similar to this, but using per-probe microarray data, is provided as Additional file 5.