Correlation between direct and reconstructed ratios. Ratio plots from Kidney vs. Breast comparisons are shown. Upper panels: scatter plots between direct ratios and each of the three reconstructed ratios (RefOligo, RefPool, One-Color). Lower panels: scatter plots between the reconstructed ratios. Ratio plots for the remaining tissue comparisons are shown as supplementary material [see Additional file 2]. In all cases, only ratios from spots with intensity values 2 SD above the average slide background were used.