High density oligonucleotide arrays are usually annotated in a one-to-one fashion, with each probeset assigned to one gene. However, in reality, subsets of oligonucleotides in a probeset may match sequences within more than one gene, potentially leading to misinterpretations. Moreover, a gene is often represented by more than one probeset, and analyzing probe matches at the mRNA level can help one deduce whether these probesets are derived from the same or different splice variants.