Microarray Technologies

The Affymetrix GeneChip oligonucleotide array contains several thousand
ssDNA oligonucleotide probe pairs. Each probe pair consists of an element
containing oligonucleotides that perfectly match the target (PM probe) and an
element containing oligonucleotides with a single base mismatch (MM probe).
A probe set consists of a set of probe pairs corresponding to a target gene.
Similarly, the labeled RNA is extracted from sample cell and hybridizes to its
complementary sequence. The expression level is measured by determining the
difference between the PM and MM probes. Then, for each gene (i.e., probe
set) average difference or log average can be calculated, in which the average
difference is defi ned as the average difference between the PM and MM of
every probe pair in a probe set and log average is defi ned as the average log
ratios of the PM/MM intensities for each probe pair in a probe set.