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Repeatability of published microarray gene expression analyses

Abstract

Given the complexity of microarray-based gene expression studies, guidelines encourage transparent design and public data availability. Several journals require public data deposition and several public databases exist. However, not all data are publicly available, and even when available, it is unknown whether the published results are reproducible by independent scientists. Here we evaluated the replication of data analyses in 18 articles on microarray-based gene expression profiling published in Nature Genetics in 2005–2006. One table or figure from each article was independently evaluated by two teams of analysts. We reproduced two analyses in principle and six partially or with some discrepancies; ten could not be reproduced. The main reason for failure to reproduce was data unavailability, and discrepancies were mostly due to incomplete data annotation or specification of data processing and analysis. Repeatability of published microarray studies is apparently limited. More strict publication rules enforcing public data availability and explicit description of data processing and analysis should be considered.

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Gene Expression Omnibus

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Author information

Authors and Affiliations

Authors

Contributions

The protocol was designed with discussion among all authors. All authors except V.v.N. participated in evaluations of the eligible articles and their analyses. V.v.N. collected all the evaluations and examined if there were discrepancies among teams. J.P.A.I. wrote the manuscript, which was critically revised by all other coauthors. After the first author, the author order is alphabetical.

Corresponding author

Correspondence to John P A Ioannidis.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1 and 2, Supplementary Table 1 (PDF 323 kb)

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Ioannidis, J., Allison, D., Ball, C. et al. Repeatability of published microarray gene expression analyses. Nat Genet 41, 149–155 (2009). https://doi.org/10.1038/ng.295

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  • DOI: https://doi.org/10.1038/ng.295

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