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Fig. 1. Two general experimental designs often employed by studies using
heterologous hybridization to microarrays. In the first design (A), samples
from two different species (species 2 and 3) are competitively hybridized
against one another to a microarray generated from oligonucleotides or cDNAs
from a single species (species 1). Note that, in some cases, species 1 may be
the same as either 2 or 3. In this design, the sequence distance between
species 1 and 2 will differ, to some degree, from that between 1 and 3; if
this difference is too great, it may affect hybridization kinetics, which may
in turn artificially affect the generated gene expression values. Under the
second design (B), the two hybridized samples are always from the same
species, and the two samples generally differ in another variable, e.g.
treatment, time point or tissue. With this design, the only sequence
divergence factor is that between species 1 and 2, and this factor should
affect both hybridized samples equally.
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