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Gene expression

Do microarrays match up?

Nature Reviews Genetics volume 6, pages 432–433 (2005)Cite this article

One of the main issues when comparing microarray data is consideration of the metrics generated by different technology platforms. There is a tremendous choice of platforms available and much diversity in protocols for sample preparation, imaging and analysis. Furthermore, whereas some groups report the absolute level of expression of a particular gene, others compare the relative transcription of genes. This makes meaningful comparisons of gene-expression data from different sources challenging.

The three papers investigate different aspects of microarray reproducibility. Larkin et al. directly compared the performance of two microarray platforms — an in-house-developed two-colour cDNA array and a commercial oligonucleotide array — in a study of the effects of chronic and acute exposure of angiotensin II on cardiac gene expression in mice. Irizarry et al. studied the impact of inter-laboratory variation by providing a consortium of ten laboratories with an identical RNA sample processed according to individual laboratory protocols, and then comparing the results obtained from three widely used microarray platforms. Finally, the Toxicogenomics Research Consortium (TRC) used in-house and commercial microarrays with identical RNA samples to assess the variability caused by sample handling, imaging and data analysis.

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ORIGINAL RESEARCH PAPERS

  1. Larkin, J. E. et al. Independence and reproducibility across microarray platforms. Nature Methods 2, 337–343 (2005)

    Article  CAS  Google Scholar 

  2. Irizarry, R. A. et al. Multiple-laboratory comparison of microarray platforms. Nature Methods 2, 345–349 (2005)

    Article  CAS  Google Scholar 

  3. Members of the Toxicogenomics Research Consortium. Standardizing global gene expression analysis between laboratories and across platforms. Nature Methods 2, 351–356 (2005)

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  1. Nature Reviews Drug Discovery,

    Joanna Owens

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  1. Joanna Owens
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Owens, J. Do microarrays match up?. Nat Rev Genet 6, 432–433 (2005). https://doi.org/10.1038/nrg1629

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