Correlation heatmap of all replicate pool pairs. RIGHT: Heatmap of Pearson correlations between replicate pairs of pooled-tumour control samples highlights the inter-run and inter-chip variation; particularly at the inter-chip level. Red cells correspond to ~96% correlation and white to 100% correlation. Batches and sample numbers are consistent with the colouring and labelling in Figures 1 and Additional File 2. A: detection filtered (DF); B: DF & quantile normalised (QN); C: DF & QN &ComBat(by run); D: DF & QN &ComBat(by chip). LEFT: Variance estimates at various levels in replicate pooled-controls hybridised to the HT-12 chips used in experiment 2. Highlights the effect of various normalisation procedures on these variance estimates; as before, such procedures include detection-filtered (DF), quantile normalised (QN), ComBat corrected by run (CB(run)), and ComBat corrected by BeadChip (CB(chip)).