Distribution of the differences between replicate pairs of intra- and inter run intensity measurements. All possible combinations of differences between replicate pairs of UHRR controls and clinical samples were compared across the five runs. Axis labels represent the difference between duplicate samples (δ) on the x-axis, against frequency (ν) on the y-axis. Values on the left of each distribution represent the standard deviation and values on the right represent the mean of the measured differences. The four columns illustrate the effect of normalisation or batch correction on these differences. The four rows of plots illustrate both inter- and intra-run differences for both UHRR and tumour samples; row 'A' contains inter-run differences calculated between the 128 pairs of UHRR samples; row 'B' corresponds to intra-run differences between the 25 pairs of UHRR; row 'C' is the inter-run differences in the 56 pairs of tumour samples; and row 'D' contains data for the intra-run differences in 7 pairs of tumour samples in Run 5.