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PubMed · 15350198

Handling multiple testing while interpreting microarrays with the Gene Ontology Database.

Michael V Osier·Hongyu Zhao·Kei-Hoi Cheung
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Abstract

BACKGROUND: The development of software tools that analyze microarray data in the context of genetic knowledgebases is being pursued by multiple research groups using different methods. A common problem for many of these tools is how to correct for multiple statistical testing since simple corrections are overly conservative and more sophisticated corrections are currently impractical. A careful study of the nature of the distribution one would expect by chance, such as by a simulation study, may be able to guide the development of an appropriate correction that is not overly time consuming computationally. RESULTS: We present the results from a preliminary study of the distribution one would expect for analyzing sets of genes extracted from Drosophila, S. cerevisiae, Wormbase, and Gramene databases using the Gene Ontology Database. CONCLUSIONS: We found that the estimated distribution is not regular and is not predictable outside of a particular set of genes. Permutation-based simulations may be necessary to determine the confidence in results of such analyses.

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AnimalsComputational BiologyData Interpretation, StatisticalDatabases, GeneticDrosophilaGene Expression ProfilingHelminthsOligonucleotide Array Sequence AnalysisSaccharomyces cerevisiaeSoftwareJournal ArticleResearch Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.

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Michael V Osier, Hongyu Zhao, Kei-Hoi Cheung. 2004-09-06. Handling multiple testing while interpreting microarrays with the Gene Ontology Database.. https://doi.org/10.1186/1471-2105-5-124

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