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also important to ensure that the probe has been sufficiently denatured before
hybridization.
9. A global normalization of all samples in addition to individual chip normal-
ization should be performed. The reference strain should display a 45 ° scatter
plot whereas the test strain should display a skewed histogram toward the
negative. GeneSpring can be used to construct a dendrogram and run a Pearson
correlation to determine whether the replicate hybridization experiments are in
agreement.
10. The Pearson correlation coefficient is used to represent the scale of a dendrogram
constructed with TreeView after phylogenetic analysis with Cluster. For a
pairwise comparison, a coefficient of 1 indicates absolute identity and zero
indicates complete independence.
Acknowledgments
The authors are grateful to Dan Sturdevant for providing technical infor-
mation.
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