Abstract: The invention features an array comprising at least one set of nucleic acid probes for detection of gene products that are produced by mRNA splicing of a selected gene, wherein each probe set is specific for a selected gene, and wherein the probe set minimally comprises a splice junction probe and either an intron probe or an exon probe. The splice junction probe hybridizes specifically to a sequence corresponding to a preselected, non-genomic sequence present in a product of mRNA splicing, while the intron probe hybridizes specifically to a sequence corresponding to an intronic sequence present in unspliced mRNA. The exon probe hybridizes specifically to a sequence corresponding to an exonic sequence of the gene. The intron probe and the exon probe may each serve as an internal control. The invention also features methods of using the array to analyze mRNA splice products in a sample.