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. Author manuscript; available in PMC: 2008 Apr 1.
Published in final edited form as: Comput Biol Chem. 2007 Feb 20;31(2):92–98. doi: 10.1016/j.compbiolchem.2007.02.008

Fig. 5.

Fig. 5

Effects of changing tb or ΔGss-cutoff on the performance of the PSAA model. Effects of changing (A) the values of tb while holding ΔGss-cutoff = -3.6 or (B) the values of ΔGss-cutoff while holding tb = 0.35 on the performance of PSAA: the position-dependent secondary-structure attenuated affinity model (Eq. 6). Data shown are for the human genome U133 Latin Square Experiment 2 Replicate 1 PM probes. NM: Naef and Magnasco (Naef and Magnasco, 2003) model (Eq. 5). The suffixes (-SH) and (-RD) indicates the R2 after generating the minimum folding energy (ΔGss) and the minimum energy structure from shuffled and random sequences, respectively (see section 3.3 for explanation).