Affymetrix 3 GeneChip microarrays are widely used to profile the expression of thousands of genes simultaneously. They differ from many other microarray types in that GeneChips are hybridised using a single labelled extract and because they contain multiple match and mismatch sequences for each transcript. Most algorithms extract the signal from GeneChip experiments in a sequence of separate steps, including background correction and normalisation, which inhibits the simultaneous use of all available information. They principally provide a point estimate of gene expression and, in contrast to BGX, do not fully integrate the uncertainty arising from potentially heterogeneous responses of the probes.