The authors acknowledge that the ability to detect differential splicing depends on various factors, including the number of probes covering the gene and the nature of the splicing event. They constructed a new statistical method, called FIRMAGene, that uses information about adjacent poorly fitting probes to calculate differential expression in the Gene arrays and showed that it provides comparable results to the Exon array analysis. The approach can only be used in well-annotated genes and can detect differential splicing involving multiple exons. However, they suggested that it should work particularly well for genes containing few exons, since for these genes the coverage of probes in the Gene platform can be greater than the Exon platform.

Dr Robinson added that, "To the best of our knowledge, this is the first statistical method that interrogates differential splicing using the Gene 1.0 ST platform. We have used this method for uncovering differential splicing in human tissues, where typically a small number of tissues exhibit a distinct pattern. However, we believe it could be useful in a variety of experimental settings." FIRMAGene can be applied to human, mouse and rat samples, for which the latest Affymetrix Gene 1.0 ST platforms are available, or any other whole-transcript microarray design.

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