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Probe-level estimation improves the detection of differential splicing in Affymetrix exon array studies

Essi Laajala1, Tero Aittokallio12, Riitta Lahesmaa1 and Laura L Elo12*

Author Affiliations

1 Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, FI-20521, Finland

2 Department of Mathematics, University of Turku, Turku, FI-20014, Finland

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Genome Biology 2009, 10:R77  doi:10.1186/gb-2009-10-7-r77

Published: 16 July 2009

Abstract

The recent advent of exon microarrays has made it possible to reveal differences in alternative splicing events on a global scale. We introduce a novel statistical procedure that takes full advantage of the probe-level information on Affymetrix exon arrays when detecting differential splicing between sample groups. In comparison to existing ranking methods, the procedure shows superior reproducibility and accuracy in distinguishing true biological findings from background noise in high agreement with experimental validations.