Pairwise Comparisons of Different Normalized Data Sets. Pairwise comparisons between the three different normalization methods and the non-normalized dataset. The graphs represent the log variance ratios for each gene versus its average Ct value. The red line is the smoothed lowess curve that captures the overall trend of the data in the plot. The dotted blue line represents horizontal axis. The direction of the ratio is reflected in each individual figure title, e.g. the ratios in Figure 3.3A are constructed by taking the log2 transformation of the GAPDH-normalized variance divided by the non-normalized variance for each gene. Points below the dotted blue line correspond to those genes where single gene GAPDH normalization has resulted in a greater reduction in variance relative to the variance of these genes in the non-normalized data.