In the relatively few years since their inception, DNA microarrays and Affymetrix GeneChips have gained increasing use and acceptance in the study of genetic and cellular processes. This is evident from the rising number of published literature citing microarrays each year. With time, gene chips and microarrays have matured into complex technologies as biologists have teamed with applied mathematicians and statisticians to increase the rigor of experimentation and address the problems associated with the manipulation of large data sets. Several complementary microarray technologies for measuring gene expression are now routinely employed. This review will discuss the similarities and differences among these technologies and cover recent efforts to integrate data from cross-platform comparative studies.