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Figure 11 | BMC Bioinformatics

Figure 11

From: Washing scaling of GeneChip microarray expression

Figure 11

Effect of re-labelling of array A on the total intensity distributions of the PM and MM probes (panel a) and on the hook curves (panel b): The data refer to the second scan A2(2x) (see Figure 1). The distributions and hook curves shift to the right after re-labelling as indicated by the grey arrows. This shift applies also to the saturation intensity: M(1st series)→M(2nd series). The latter value exceeds the maximum detectable intensity of the scanner, i.e. Omax < M(2nd). This constraint truncates the intensity distributions at Omax and sets all intensity values greater than the optical limit equal to Omax which causes the small peak at the right end of the distribution. Note that the width of the hooks remains virtually the same in both series whereas its height slightly increases after re-labelling. This result suggests that labelling with SAPE facilitates the washing-off of probe-bound targets. The washing-time kinetics of the hook-parameters is shown in Figure 12.

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