Methodology article
Reproducibility of gene expression across generations of Affymetrix microarrays
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* Corresponding author: Ashish Nimgaonkar ashish@chip.org
- † Equal contributors
1 Informatics Program, Children's Hospital, Harvard Medical School, Boston, MA, USA
2 Division of Health Sciences and Technology, Harvard University and MIT, Cambridge, MA, USA
3 Genetics Division, Children's Hospital, Harvard Medical School, Boston, MA, USA
BMC Bioinformatics 2003, 4:27 doi:10.1186/1471-2105-4-27
Published: 25 June 2003Abstract
Background
The development of large-scale gene expression profiling technologies is rapidly changing the norms of biological investigation. But the rapid pace of change itself presents challenges. Commercial microarrays are regularly modified to incorporate new genes and improved target sequences. Although the ability to compare datasets across generations is crucial for any long-term research project, to date no means to allow such comparisons have been developed. In this study the reproducibility of gene expression levels across two generations of Affymetrix GeneChips® (HuGeneFL and HG-U95A) was measured.
Results
Correlation coefficients were computed for gene expression values across chip generations based on different measures of similarity. Comparing the absolute calls assigned to the individual probe sets across the generations found them to be largely unchanged.
Conclusion
We show that experimental replicates are highly reproducible, but that reproducibility across generations depends on the degree of similarity of the probe sets and the expression level of the corresponding transcript.