Exons, introns and  splicing of mRNA, discovered in the late 1970s, is a process which adds considerable complexity to the human genome. In addition to other forms of regulation of gene expression (chromatin, transcriiptional, degredation, sequestration, etc) alternative splicing allows the gene to produce not just one, but from 2 to 10,000+ distinct protein products by selecting alternative subsets of exons, thus allowing the roughly 30,000 human genes to produce 100,000 or more proteins, as and where needed.  The Affymetrix Human Exon 1.0 ST array includes about 1.4 million probesets, more than enough to cover an estimated 1 million human exons, and allows for measurement of gene expression and potentially, discovery of known and novel alternative splicing events We have addressed several significant statistical and bioinformatics problems encountered in analyzing data from this microarray. While the chip can indeed detect the occurrence of alternative splicing, it is not always possible to determine the particular pattern of splicing which gives rise to the observed data.  We present several potential solutions to problems encountered in the analysis of such data.