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http://hdl.handle.net/1942/9006
Title: | An Investigation on Performance of Significance Analysis of Microarray (SAM) for the Comparisons of Several Treatments with one Control in the Presence of Small-variance Genes | Authors: | LIN, Dan SHKEDY, Ziv BURZYKOWSKI, Tomasz Ion, R. Goehlmann, H.W.H. De Bondt, A. Perera, T. Geerts, T. Van den Wyngaert, I. BIJNENS, Luc |
Issue Date: | 2008 | Publisher: | WILEY-V C H VERLAG GMBH | Source: | 5th International Conference on Multiple Comparison Procedures. BIOMETRICAL JOURNAL, 50(5) Spec. iss, p. 801-823. | Series/Report: | BIOMETRICAL JOURNAL | Series/Report no.: | 50(5) Spec. iss. | Abstract: | One of multiple testing problems in drug finding experiments is the comparison of several treatments with one control. In this paper we discuss a particular situation of such an experiment, i.e., a microarray setting, where the many-to-one comparisons need to be addressed for thousands of genes simultaneously. For a gene-specific analysis, Dunnett's single step procedure is considered within gene tests, while the FDR controlling procedures such as Significance Analysis of Microarrays (SAM) and Benjamini and Hochberg (BH) False Discovery Rate (FDR) adjustment are applied to control the error rate across genes. The method is applied to a microarray experiment with four treatment groups (three microarrays in each group) and 16,998 genes. Simulation studies are conducted to investigate the performance of the SAM method and the BH-FDR procedure with regard to controlling the FDR, and to investigate the effect of small-variance genes on the FDR in the SAM procedure. | Notes: | [Lin, D.; Shkedy, Z.; Burzykowski, T.] Hasselt Univ, Ctr Stat, B-3590 Diepenbeek, Belgium. [Ion, R.; Goehlmann, H. W. H.; De Bondt, A.; Perera, T.; Geerts, T.; Van den Wyngaert, I.; Bijnens, L.] Johnson & Johnson Pharmaceut Res & Dev, B-2340 Beerse, Belgium. | Keywords: | Benjamini and Hochberg procedure; Dunnett's single step procedure; False Discovery Rate (FDR); Microarray; Multiple testing; SAM | Document URI: | http://hdl.handle.net/1942/9006 | ISSN: | 0323-3847 | e-ISSN: | 1521-4036 | DOI: | 10.1002/bimj.200710467 | ISI #: | 000260698100017 | Category: | C1 | Type: | Proceedings Paper | Validations: | ecoom 2009 |
Appears in Collections: | Research publications |
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File | Description | Size | Format | |
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An Investigation on Performance of Significance Analysis.pdf | Peer-reviewed author version | 1.11 MB | Adobe PDF | View/Open |
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