(a) Cumulative distribution of Δlog2 fold changes. (b) Bland-Altman plot for log2 fold changes. The difference in log2 fold change measured with both methods is plotted against the average of these log2 fold changes. The 95% confidence interval of the true difference is delineated by the upper (ULA) and lower limit of agreement (ULA). (c) Enrichment analysis. Each data point in the cumulative distribution plot of Δlog2 fold changes results from two log2 fold changes, each calculated from two log2 relative quantities that both in turn result from five Cq values (one gene of interest and four reference genes). Data points in purple are data points for which at least 1 of the 20 Cq values giving rise to this data point is higher than the specified cutoff.