Figure 2

Exemplar graph to clarify the interpretation of Figure 3. The graph presents a visual pairwise comparison between two normalization algorithms Q₁ and Q₂ on the same data set. For each gene, we calculate the variance of its Q₁-normalized expression profile and its Q₂-normalized expression profile and plot the log₂-ratio of this variance on the y-axis where Y = log₂ [Q₁-normalized: Q₂-normalized]. A gene's log variance ratio is plotted against its expression (mean Ct value) on the x-axis. The regions where the data points fall in the graph give us an indication of which normalization algorithm produces noisier data and whether there is a differential bias in expression for genes most affected by this noise.