Exon Array Background Correction

MM probes provide controls similar in sequence and location which are useful in removing bias; this takes one probe per informative probe. Because the MM probes hybridize to the perfect match (PM) target, when MM intensities are subtracted from PM intensities the PM response to true target slightly reduced. BGP probes provide a rough estimate of background based on coarsely modeled sequence, without taking into account any spatial variation. Use of BGP over MM probes requires roughly 50% less space on the array; thus use of BGP probes allows roughly a 2 fold increase in PM content.