Figure 1.

Dependence of the variance on the mean for condition A in the fly RNA-Seq data. (a) The scatter plot shows the common-scale sample variances (Equation (7)) plotted against the common-scale means (Equation (6)). The orange line is the fit w(q). The purple lines show the variance implied by the Poisson distribution for each of the two samples, that is, ${\widehat{s}}_j{\widehat{q}}_{i,A}$. The dashed orange line is the variance estimate used by edgeR. (b) Same data as in (a), with the y-axis rescaled to show the squared coefficient of variation (SCV), that is all quantities are divided by the square of the mean. In (b), the solid orange line incorporated the bias correction described in Supplementary Note C in Additional file 1. (The plot only shows SCV values in the range [0, 0.2]. For a zoom-out to the full range, see Supplementary Figure S9 in Additional file 1.)