  Tiling arrays make possible a large scale exploration of the genome thanks to
probes which cover the whole genome with very high density until 2 000 000
probes. Biological questions usually addressed are either the expression
difference between two conditions or the detection of transcribed regions. In
this work we propose to consider simultaneously both questions as an
unsupervised classification problem by modeling the joint distribution of the
two conditions. In contrast to previous methods, we account for all available
information on the probes as well as biological knowledge like annotation and
spatial dependence between probes. Since probes are not biologically relevant
units we propose a classification rule for non-connected regions covered by
several probes. Applications to transcriptomic and ChIP-chip data of
Arabidopsis thaliana obtained with a NimbleGen tiling array highlight the
importance of a precise modeling and the region classification.
