Exon Array Background Correction

Abstract

We expect to obtain similar performance in detection of differential changes for most applications on exon arrays using the background probe collection (BGP) as opposed to specific mismatch probes (MM). (For example, the GeneChip® Human Exon 1.0 ST Array has a “genomic” and an “antigenomic” background probe collection. See Appendix for more information on the background probe collections.) In this whitepaper BGP probes are used to perform a PM-GCBG correction. PM- GCBG refers to the use of the median BGP intensity for BGP probes with the same GC content as the perfect match (PM) probe.