  We analyze a series of publicly available controlled experiments (Latin
square) on Affymetrix high density oligonucleotide microarrays using a simple
physical model of the hybridization process. We plot for each gene the signal
intensity versus the hybridization free energy of RNA/DNA duplexes in solution,
for perfect matching and mismatching probes. Both values tend to align on a
single master curve in good agreement with Langmuir adsorption theory, provided
one takes into account the decrease of the effective target concentration due
to target-target hybridization in solution. We give an example of a deviation
from the expected thermodynamical behavior for the probe set 1091\_at due to
annotation problems, i.e. the surface-bound probe is not the exact complement
of the target RNA sequence, because of errors present in public databases at
the time when the array was designed. We show that the parametrization of the
experimental data with RNA/DNA free energy improves the quality of the fits and
enhances the stability of the fitting parameters compared to previous studies.
