New methods have been developed for determining and monitoring gene expression levels during pathologic or therapeutic processes. In particular, nucleic acid microarrays provide information about the expression levels of thousands of genes during a single experiment. Advances in nucleic acid sequencing technology and the subsequent burgeoning of public sequence databases have resulted in the availability of a vast amount of sequence information for both known genes and expressed sequence tags (ESTs). These data have been used in the design and creation of clone sets utilized as probes during microarray expression profiling analysis. Several different microarray platforms exist, which make use of either oligonucleotides or cDNA amplification products spotted onto solid or semisolid substrates. Perhaps the most well known use of oligonucleotides for microarray analysis is the GeneChip™ system (Affymetrix Inc., Emeryville, CA). A GeneChip™ consists of a silicon wafer containing hundreds of thousands of oligonucleotide probe sets designed to interrogate specific genes. To control for nonspecific hybridization, two different probe sets are created to interrogate each gene. One probe set matches the target sequence perfectly and is called the “perfect match” (PM). The other probe set, known as the “mismatch” (MM) is identical to the “perfect match” set, with the exception that there is a single nucleotide mismatch in the center position of each probe.