Sample size for identifying differentially expressed genes in microarray experiments

Journal of Computational Biology

Volumn 11, Issue 4, 2004, Pages 714-726

  Wang, Sue Jane ^a   Chen, James J ^b  

^a CENTER FOR DRUG EVALUATION AND RESEARCH   (United States)

^b NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH   (United States)

Author keywords

Number of arrays; One and two sample t tests; Power; Replicate; Standardized effect size

Indexed keywords

ARTICLE; CALCULATION; DNA MICROARRAY; DNA REPLICATION; GENE EXPRESSION; GENE IDENTIFICATION; INTERMETHOD COMPARISON; MUTATION; PRIORITY JOURNAL; SAMPLE SIZE; SIMULATION; STATISTICAL MODEL;

ANIMALS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; KIDNEY; MODELS, STATISTICAL; MONTE CARLO METHOD; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RATS; RNA, MESSENGER; SAMPLE SIZE; TOXICOGENETICS;

EID: 4544298732     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2004.11.714     Document Type: Article

References (18)

1. Benjamini, Y., and Hochberg, Y. 1995. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. Roy. Stat. Soc. B 57, 289-300.
2. Black, M.A., and Doerge, R.W. 2002. Calculation of the Minimum Number of Replicate Spots Required for Detection of Significant Gene Expression Fold Changes for cDNA Microarrays. Technical Report, Department of Statistics, Purdue University, IN.
3. Chen, Y.-J., Kodell, R.L., Sistare, F., Thompson, K., Morris, S., and Chen, J.J. 2002. Normalization methods for cDNA microarray data analysis. J. Biopharm. Stat. 13, 56-74.
4. Donovan, D.M., and Becker, K.G. 2002. Double round hybridization of membrane based cDNA arrays: Improved background reduction and data replication. J. Neuros. Methods 118, 59-62.
5. Draghici, S., Kuklin, A., Hoff, B., and Shams, S. 2001. Experimental design, analysis of variance and slide quality assessment in gene expression array. Drug Discovery Devel. 4(3), 332-337.
6. Dudoit, S., Yang, Y.H., Callow, M.J., and Speed, T.P. 2002. Statistical methods for identifying differential expressed genes in replicated cDNA microarray experiments. Statistica Sinica 12, 111-139.
7. Herwig, R., Aanstad, P., Clark, M., and Lehrach, H. 2001. Statistical evaluation of differential expression on cDNA nylon arrays with replicated experiments. Nucl. Acids. Res. 29(23), e117.
8. Hochberg, Y., and Tamahane, A.C. 1987. Multiple Comparison Procedures, John Wiley, New York.
9. Holm, S. 1979. A simple sequentially rejective multiple test procedure. Scand. J. Statist. 6, 65-70.
10. Kerr, M.K., Martin, M., and Churchill, G.A. 2000. Analysis of variance for gene expression microarray data. J. Comp. Biol. 7, 819-837.
11. Lee, M.-L.-T., Kuo, F.C., Whitmore, G.A., Sklar, J.L. 2000. Importance of replication in microarray gene expression studies. Statis. Sci. 97, 9834-9839.
12. Pan, W., Lin, J., and Le, C.T. 2002. How many replicates of arrays are required to detect gene expression changes in microarray experiments? A mixture model approach. Genome Biol. 3(5), 0022.1-0022.10.
13. Tsai, C.A., Chen, Y.J., and Chen, J.J. 2003. Testing for differentially expressed genes with microarray data. Nucl. Acids Res. 31(9), e52.
14. Van Der Laan, M.J, and Bryan, J. 2001. Gene expression analysis with the parametric bootstrap. J. Biostatist. 2, 445-461.
15. Westfall, P.H., and Young, S.S. 1993. Resampling-Based Multiple Testing, John Wiley, New York.
16. Wolfinger, R.D., Gibson G., and Wolfinger, E.D. 2001. Assessing gene significance from cDNA microarray expression data via mixed models. J. Comp. Biol. 8, 625-637.
17. Yang, Y.W., Dudoit S., Luu, P., Peng, V., Ngai, J., and Speed, T.P. 2002. Normalization of cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation. Nucl. Acids Res. 30(4), e15.
18. Zien, A., Fluck, J., Zimmer, R., and Lengauer, T. 2002. Microarrays: How many do you need? RECOMB 2002.