Handling multiple testing while interpreting microarrays with the Gene Ontology Database
<p>Abstract</p> <p>Background</p> <p>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...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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BMC
2004-09-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/5/124 |
| _version_ | 1811314716099739648 |
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| author | Zhao Hongyu Osier Michael V Cheung Kei-Hoi |
| author_facet | Zhao Hongyu Osier Michael V Cheung Kei-Hoi |
| author_sort | Zhao Hongyu |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>We present the results from a preliminary study of the distribution one would expect for analyzing sets of genes extracted from <it>Drosophila</it>, <it>S. cerevisiae</it>, Wormbase, and Gramene databases using the Gene Ontology Database.</p> <p>Conclusions</p> <p>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.</p> |
| first_indexed | 2024-04-13T11:16:21Z |
| format | Article |
| id | doaj.art-36ec8fe1181c4aff8c7c03b23120e5a4 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-13T11:16:21Z |
| publishDate | 2004-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-36ec8fe1181c4aff8c7c03b23120e5a42022-12-22T02:48:56ZengBMCBMC Bioinformatics1471-21052004-09-015112410.1186/1471-2105-5-124Handling multiple testing while interpreting microarrays with the Gene Ontology DatabaseZhao HongyuOsier Michael VCheung Kei-Hoi<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>We present the results from a preliminary study of the distribution one would expect for analyzing sets of genes extracted from <it>Drosophila</it>, <it>S. cerevisiae</it>, Wormbase, and Gramene databases using the Gene Ontology Database.</p> <p>Conclusions</p> <p>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.</p>http://www.biomedcentral.com/1471-2105/5/124 |
| spellingShingle | Zhao Hongyu Osier Michael V Cheung Kei-Hoi Handling multiple testing while interpreting microarrays with the Gene Ontology Database BMC Bioinformatics |
| title | Handling multiple testing while interpreting microarrays with the Gene Ontology Database |
| title_full | Handling multiple testing while interpreting microarrays with the Gene Ontology Database |
| title_fullStr | Handling multiple testing while interpreting microarrays with the Gene Ontology Database |
| title_full_unstemmed | Handling multiple testing while interpreting microarrays with the Gene Ontology Database |
| title_short | Handling multiple testing while interpreting microarrays with the Gene Ontology Database |
| title_sort | handling multiple testing while interpreting microarrays with the gene ontology database |
| url | http://www.biomedcentral.com/1471-2105/5/124 |
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