Figure 9

Differential effect of washing between PM and MM probes (part a) and between specific and nonspecific binding (part b): Differences are calculated from the intensities after 17 washing cycles (t = 17) relative to the unwashed chip (t = 0). Panel a illustrates the Δ-coordinates Δ(0) and Δ(17) as a function of the mean intensity Σ(0) and their difference Δ(17) - Δ(0). It shows the typical hook-like shape indicating maximum washing effect on the PM/MM log-intensity difference in the mix-hybridization range. The effect is markedly reduced in the sat- and as-ranges because specific transcripts bind relatively strongly to both PM and MM, strongly reducing their washing efficiency. The PM/MM-ratio of the limiting saturation intensities is given by δα^S~0.2 (see also Eq. (28) in the Methods-section). The difference in washing effects virtually disappears in the N-range because the weakly bound nonspecific transcripts are washed off from the PM and MM probes in nearly identical amounts (i.e. δα^N~0). Panel b correlates the Σ-coordinates at t = 0 and t = 17. The lower plot shows the difference Σ(17) - Σ(0). The washing effect on the mean intensity is maximum in the N-range (δβ^N~-0.95, see Eq. (27)). It gradually decreases with increasing contribution of specific hybridization to about δβ^S~-0.13.