Figure 2

Normalizing and centering probe intensity data. Data transformation steps used to normalize and center data from A) initial raw probe intensity, to B) adjusted for thermodynamic binding affinity (ΔG₃₇ ), to C) centering of median control probes, in comparison to D) quantile normalization. Data are graphed for Caenorhabditis elegans N2 (blue), C. elegans CB4856 (green), C. briggsae (red), and non-Caenorhabditis species (black), but note that quantile normalized signals (D) are relative to homologous hybridization, so no data for N2 is shown. Left column: signals from control probes only (from Arabidopsis thaliana and Bacillus subtilis sequences); right column: signals from exon probes only.