The majority of commercial GeneChip® expression arrays are antisense arrays - they interrogate targets that are prepared in the antisense orientation. The E.coli Genome Array is an exception; it was designed in the sense orientation. Therefore, there are three basic types of expression assays:

1. cRNA target amplification and labeling assay - Used for all eukaryotic GeneChip expression arrays.
2. Direct labeling of enriched RNA: used specifically for E.coli Genome Array
3. cDNA target labeling assay: used for other prokaryotic GeneChip expression arrays