  In the past couple of years several studies have shown that hybridization in
Affymetrix DNA microarrays can be rather well understood on the basis of simple
models of physical chemistry. In the majority of the cases a Langmuir isotherm
was used to fit experimental data. Although there is a general consensus about
this approach, some discrepancies between different studies are evident. For
instance, some authors have fitted the hybridization affinities from the
microarray fluorescent intensities, while others used affinities obtained from
melting experiments in solution. The former approach yields fitted affinities
that at first sight are only partially consistent with solution values. In this
paper we show that this discrepancy exists only superficially: a sufficiently
complete model provides effective affinities which are fully consistent with
those fitted to experimental data. This link provides new insight on the
relevant processes underlying the functioning of DNA microarrays.
