Fig. 2

ERCC signal response as a function of relative abundance in each of the four pools on the Illumina microarray platform. In Panel a, each line represents an individual ERCC control, where grey = titrated, black = 1-to-1, red = outlier, and dashed-line = background (average ERCC-00073). In Panel b, the centroid of each ERCC control is plotted, where the red line corresponds to the fitted Langmuir model, open circles = within 99 % CI, red circles = outliers, and dashed-line = background. In Panel c, the slope of each ERCC is plotted, where the red line corresponds to expected slope (first derivative of the Langmuir model), the vertical dotted lines correspond to the margins of the linear region (inflection points of the first derivative of the Langmuir model), the open circles = monotonic ERCC controls (ρ = 1), grey squares = non-monotonic, and red = outliers. Numbers adjacent to outliers in Panels b and c correspond to the last three digits of the Control ID in Table 3. In Panel d, each ERCC control is represented on the Bland-Altman plot of Pool 12 vs Pool 14, where the red line corresponds to the ratio versus average intensity derived from the fitted Langmuir model, with outliers coded as in Panels b and c above