- Affymetrix arrays
- Affymetrix is a leading manufacturer of oligonucleotide arrays (http://www.Affymetrix.com/). Affymetrix expression arrays use a set of features (often referred to as -Y΄spots‘) designed to recognize each molecule of interest. Each feature consists of millions of identical single-stranded 25-mer nucleotide probes, each designed to hybridize to a specific transcript. On a gene-level array, each of these Perfect Match (PM) features is accompanied by an adjacent Mis-Match (MM) feature in which the middle residue is changed. Hybridization conditions are designed to maximise binding to the PM features while minimizing binding to the MM ones. Each MM feature can therefore be used to provide a measure of probe specific background for its PM partner. Multiple PM/MM pairs are used for each transcript. On most gene-level arrays, 11 PM/MM pairs are used per transcript, and the complete set of 22 features is referred to as a probeset.