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Open Access Highly Accessed Research article

Comparison of the latest commercial short and long oligonucleotide microarray technologies

Aurélien de Reyniès1, Daniela Geromin12, Jean-Michel Cayuela2, Fabien Petel1, Philippe Dessen13, François Sigaux12 and David S Rickman1*

Author Affiliations

1 Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France

2 INSERM U462 'Lymphocyte et Cancer', Institut Universitaire d'Hematologie, Hospital Saint Louis, Paris, France

3 Genetics and Oncology, UMR 8125 CNRS, Institute Gustave Roussy, Villejuif, France

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BMC Genomics 2006, 7:51  doi:10.1186/1471-2164-7-51

Published: 15 March 2006



We compared the relative precision and accuracy of expression measurements obtained from three different state-of-the-art commercial short and long-oligonucleotide microarray platforms (Affymetrix GeneChip™, GE Healthcare CodeLink™ and Agilent Technologies). The design of the comparison was chosen to judge each platform in the context of a multi-project program.


All wet-lab experiments and raw data acquisitions were performed independently by each commercial platform. Intra-platform reproducibility was assessed using measurements from all available targets. Inter-platform comparisons of relative signal intensities were based on a common and non-redundant set of roughly 3,400 targets chosen for their unique correspondence toward a single transcript. Despite many examples of strong similarities we found several areas of discrepancy between the different platforms.


We found a higher level of reproducibility from one-color based microarrays (Affymetrix and CodeLink) compared to the two-color arrays from Agilent. Overall, Affymetrix data had a slightly higher level of concordance with sample-matched real-time quantitative reverse-transcriptase polymerase chain reaction (QRT-PCR) data particularly for detecting small changes in gene expression levels.