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The following HTML text is provided to enhance online readability. Many aspects of typography translate only awkwardly to HTML. Please use the page image as the authoritative form to ensure accuracy. important. These assumptions are typically not true. A list of genes of interest may be available before the microarray experiment is conducted. What FDR cutoff values to use to pick follow-up genes and how to apply the FDR adjustment will be discussed. REFERENCESAffymetrix, Inc. 2002. Statistical Algorithms Description Document [online]. Available: http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf [accessed April 10, 2006]. Baldi, P., and A.D. Long. 2001. A Bayesian framework for the analysis of microarray expression data: Regularized t-test and statistical inferences of gene changes. Bioinformatics 17(6):509-519. Benjamini, Y., and Y. Hochberg. 1995. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. B Met. 57(1):289-300. Chu, T.M., B. Weir, and R.D. Wolfinger. 2002. A systematic statistical linear modeling approach to oligonucleotide array experiments. Math. Biosci. 176(1):35-51. Cope, L.M., R.A. Irizarry, H.A. Jaffee, Z. Wu, and T.S. Speed. 2004. A benchmark for Affymetrix GeneChip expression measures. Bioinformatics 20(2):323-331. Irizarry, R.A., B. Hobbs, F. Collin, Y.D. Beazer-Barclay, K.J. Antonellis, U. Scherf, and T.P. Speed. 2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4(2):249-264. Li, C., and W.H. Wong. 2001. Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. Proc. Natl. Acad. Sci. USA 98(1):31-36. Tusher, V.G., R. Tibshirani, and G. Chu. 2001. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA 98(18):5116–5121.
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