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Bioinformatics Advance Access originally published online on July 15, 2004
Bioinformatics 2004 20(18):3431-3441; doi:10.1093/bioinformatics/bth421
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Bioinformatics vol. 20 issue 18 © Oxford University Press 2004; all rights reserved.

Limited agreement among three global gene expression methods highlights the requirement for non-global validation

Peter M. Haverty 1, Li-Li Hsiao 2, Steven R. Gullans 2, Ulla Hansen 1,3 and Zhiping Weng 1,4,*

1 Bioinformatics Program, 2 Departments of Medicine and Neurology, Brigham and Women's Hospital, Harvard Medical School, 3 Department of Biology and 4 Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA

Received on December 14, 2003; revised on June 29, 2004; accepted on July 10, 2004
Advance Access Publication July 15, 2004

Motivation: DNA microarrays have revolutionized biological research, but their reliability and accuracy have not been extensively evaluated. Thorough testing of microarrays through comparison to dissimilar gene expression methods is necessary in order to determine their accuracy.

Results: We have systematically compared three global gene expression methods on all available histologically normal samples from five human organ types. The data included 25 Affymetrix high-density oligonucleotide array experiments, 23 expressed sequence tag based expression (EBE) experiments and 5 SAGE experiments. The reported gene-by-gene expression patterns showed a wide range of correlations between pairs of methods. This level of agreement was sufficient for accurate clustering of datasets from the same tissue and dissimilar methods, but highlights the need for thorough validation of individual gene expression measurements by alternate, non-global methods. Furthermore, analyses of mRNA abundance distributions indicate limitations in the EBE and SAGE methods at both high- and low-expression levels.

Contact: zhiping{at}bu.edu

* To whom correspondence should be addressed.


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