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Figure 11 | Algorithms for Molecular Biology

Figure 11

From: "Hook"-calibration of GeneChip-microarrays: Chip characteristics and expression measures

Figure 11

Characterization of the 3'/5'-amplification bias for the two samples shown in Figure 10 using the GADPH-probe sets Affx_rat_GADPH_x_at with x = 3', m and 5'. These three sets probe the GADPH-transcript with increasing distance from the 3'-end. The bars show the log-averages of the PM and MM intensities after correction for the optical background over the respective probe sets (Σ) and the MAS5 and hook (PMonly) expression estimates. The horizontal line indicates the hook-coordinate of the break, Σbreak with Σ ≥ Σbreak called present (P) and Σ < Σbreak called absent (A, see also the middle panel of Figure 10). Note that the Σ-signal of GADPH in sample A is dominated by non-specific hybridization at least for the m- and 5'-probes whereas it contains a much larger specific contribution in sample B. The fold-changes of the 3'/5'-signals are given above the 3'-bars. The circles indicate the respective Δ-coordinate of the hook-curve referring to the right axis.

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