A versatile tool to analyze GeneChip Array data at both gene and exon levels. Gene arrays were originally designed to measure genome-wide expression changes. However, their probe design also allows for the analysis of changes at the exon level to identify alternative splicing events. The applicability of GAA was demonstrated by analyzing datasets from heart development and cardiomyocyte differentiation. We were able to identify differentially expressed genes and differentially expressed exons in both datasets and illustrated how the graphical output of GAA helps to recognize different isoforms.