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Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/10000

Title: A Comparison of Procedures for Controlling the False Discovery Rate in the Presence of Small Variance Genes: A Simulation Study
Authors: LIN, Dan
SHKEDY, Ziv
BURZYKOWSKI, Tomasz
Talloen, W.
Bijnens, L.
Issue Date: 2009
Publisher: TAYLOR & FRANCIS INC
Citation: COMMUNICATIONS IN STATISTICS-SIMULATION AND COMPUTATION, 38(10). p. 2111-2122
Abstract: The Significance Analysis of Microarrays (SAM; Tusher et al., 2001) method is widely used in analyzing gene expression data while controlling the FDR by using resampling-based procedure in the microarray setting. One of the main components of the SAM procedure is the adjustment of the test statistic. The introduction of the fudge factor to the test statistic aims at deflating the large value of test statistics due to the small standard error of gene-expression. Lin et al. (2008) pointed out that the fudge factor does not effectively improve the power and the control of the FDR as compared to the SAM procedure without the fudge factor in the presence of small variance genes. Motivated by the simulation results presented in Lin et al. (2008), in this article, we extend our study to compare several methods for choosing the fudge factor in the modified t-type test statistics and use simulation studies to investigate the power and the control of the FDR of the considered methods.
Notes: [Lin, Dan] Hasselt Univ, B-3590 Diepenbeek, Belgium. [Talloen, Willem; Bijnens, Luc] J&JPRD, Beerse, Belgium.
URI: http://hdl.handle.net/1942/10000
DOI: 10.1080/03610910903249510
ISI #: 000270912700006
ISSN: 0361-0918
Category: A1
Type: Journal Contribution
Validation: ecoom, 2010
Appears in Collections: Research publications

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