Figure 11

Schematic summary of the hook-method: The raw intensity data of one GeneChip microarray are plotted into the Δ = log(PM/MM)-vs-Σ = 1/2·log(PM·MM) coordinate system and smoothed to get the raw hook-curve. Then, probes from the N- and S-hybridization regimes are used to calculate four sets of position-dependent sensitivity profiles of the affinity model (non-specific and specific for the PM and MM each) which in turn are used to correct the intensities for sequence effects. The corrected intensities provide the corrected hook-curve. The mix-, S- and sat-ranges are fitted using the two-species Langmuir hybridization model. The dimensions of the hook, its width and height, provide hybridization characteristics of the chip which in turn are used to calculate probe-level expression measures.