The AltMouse array is an older generation (2002) Affymetrix exon-exon junction microarray designed for Mus Musculus. This array probes approximately 40,000 isoform features for over 7,000 genes. AltAnalyze was initially designed for reciprocal exon-exon junction analyses for this array, however, exon array analyses were ultimately introduced first. Junction array analysis differs from exon array analysis in AltAnalyze, in that two probesets (or even possibly more when users choose to agglomerate exon/junction inclusion features) are used to assess alternative exon inclusion. Typically, the two probesets represent an inclusion and exclusion junction that measure the inclusion of one or more potential alternative exons.