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.
Darby et al. BMC Bioinformatics 2011 12:183 doi:10.1186/1471-2105-12-183