Comparison of the latest commercial short and long oligonucleotide microarray technologies.

ABSTRACT:

Background

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.

Results

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.

Conclusion

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.

SUBMITTER: de Reynies A 

PROVIDER: S-EPMC1473202 | biostudies-literature | 2006 Mar

REPOSITORIES: biostudies-literature