Reply to 'linking probe thermodynamics to microarray quantification'

We defend Langmuir-like models of microarrays from accusations by Li et al (2010 Phys. Biol. 7 048001) that they fail to link sequence-specific properties to hybridization signals. We argue that existing Langmuir-like models based on accepted principles of physical chemistry, together with a model of post-hybridization washing, are entirely consistent with various controlled experiments. Li et al's competitive hybridization model on the other hand is not verified experimentally using designs which allow for an unambiguous differentiation with respect to Langmuir-like models and exhibits no benefit in fitting microarray probe intensities.