Gene microarray analyses represent potentially effective means for high-throughput gene expression profiling in non-human primates. In the companion article, we emphasize effective experimental design based on the in vivo physiology of the rhesus macaque, whereas this article emphasizes considerations for gene annotation and data interpretation using gene microarray platforms from Affymetrix. Initial annotation of the rhesus genome array was based on Affymetrix human GeneChips. However, annotation revisions improve the precision with which rhesus transcripts are identified. Annotation of the rhesus GeneChip is under continuous revision with large percentages of probesets under multiple annotation systems having undergone multiple reassignments between March 2007 and November 2008. It is also important to consider that quantitation and comparison of gene expression levels across multiple chips requires appropriate normalization. External corroboration of microarray results using PCR-based methodology also requires validation of appropriate internal reference genes for normalization of expression values. Many tools are now freely available to aid investigators with microarray normalization and selection of internal reference genes to be used for independent corroboration of microarray results.