Advanced SearchSearch Tips
Permutation-Based Test with Small Samples for Detecting Differentially Expressed Genes
facebook(new window)  Pirnt(new window) E-mail(new window) Excel Download
 Title & Authors
Permutation-Based Test with Small Samples for Detecting Differentially Expressed Genes
Lee, Ju-Hyoung; Song, Hae-Hiang;
  PDF(new window)
In the analysis of microarray data with a small number of arrays, the most important task is the detection of differentially expressed genes by a significance test. For this purpose, one needs to construct a null distribution based on a large number of genes and one of the best way for constructing the null distribution for a small number of arrays is by means of permutation methods. In this paper we propose simple test statistics and permutation methods that are appropriate in constructing the null distribution. In a simulation study, we compare the null distributions generated by the proposed test statistics and permutation methods with the previous ones. With an example microarray data, differentially expressed genes are determined by applying these methods.
Permutation test;micorarray data;differentially expressed genes;null distribution;
 Cited by
조희진, 송혜향 (2004). 변수가 관측치보다 많은 자료에서 표식 유전자를 찾기 위한 방법, 가톨릭대학교 의과대학 의학통계학과 석사학위 논문집

Albers, W., Bickel, P. J. and van Zwet, W. R. (1976). Asymptotic expansions for the power of distribution free tests in the one-sample problem, Annals of Statistic, 4, 108-156 crossref(new window)

Alon, U., Barkai, N., Notterman, D. A., Gish, K., Ybarra, S., Mack, D. and Levine, A. J. (1999). Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays, Proceedings of the National Academy of Sciences of the United States of America, 96, 6745-6750 crossref(new window)

Chernoff, H. and Savage, I. R. (1958). Asymptotic normality and efficiency of certain nonparametric test statistics, Annals of Mathematical Statistics, 29, 972-994 crossref(new window)

Efron, B., Tibshirani, R., Storey, J. D. and Tusher, V. (2001). Empirical Bayes analysis of a microarray experiment, Journal of American Statistical Association, 96, 1151-2001 crossref(new window)

Fisher, R. A. (1935, 1966). The Design of Experiments (1st ed., 8th ed.). Oliver& Boyd, Edinburgh

Gao, X. (2006). Construction of null statistics in permutation-based multiple testing for multi-factorial microarray experiments, Bioinformatics, 22, 1486-1494 crossref(new window)

Hoeffding, W. (1952). The large-sample power of tests based on permutations of observations, Annals of Mathematical Statistics, 23, 169-192 crossref(new window)

Jain, N., Thatte, J., Braciale, T., Ley, K., O'Connel, M. and Lee, J. K. (2003). Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays, Bioinformatics, 15, 1945-1951

Lee, J.K. (2001). OAnalysis issues for gene expression array data, Clinical Chemistry, 47, 1350-1352

Lehmann, E. L. and Stein, C. (1949). On the theory of some non-parametric hypotheses, The Annals of Mathematical Statistics, 20, 28-45 crossref(new window)

Pan, W. (2003a). On the use of permutation in and the performance of a class of nonparametric methods to detect differential gene expression, Biometrics, 19, 1333-1340

Pan, W., Lin, J. and Le, C. (2003b). A mixture model approach to detecting differentially expressed genes with microarray data, Functional Integrative Genomics, 3, 117-124 crossref(new window)

Pitman, E. J. G. (1937). Significance tests which may be applied to samples from any populations, Journal of the Royal Statistical Society, 4, 119-130

Smyth, G. K., Yang, Y. H. and Speed, T. (2003). Statistical issues in cDNA microarray data analysis, Methods in Molecular Biology, 224, 111-136

Spino, C. and Pagano, M. (1991). Efficient calculation of the permutation distribution of trimmed means, Journal of the American Statistical Association, 86, 729-737 crossref(new window)

Tusher, V. G., Tibshirani, R. and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response, Proceedings of the National Academy of Sciences of the United States of America, 98, 5116-5121 crossref(new window)

Welch, W. J. (1990). Construction of permutation Tests, Journal of the American Statistical Association, 85, 693-698 crossref(new window)

Xie, Y., Pan, W. and Khodursky, A. B. (2005). A note on using permutation-based false discovery rate estiimates to compare different analysis methods for microarray data, Bioinformatics, 21, 4280-4288 crossref(new window)

Zhao, Y. and Pan, W. (2003). Modified nonparametric approaches to detecting differentially expressed genes in replicated microarray experiments, Bioinformatics, 19, 1046-1054 crossref(new window)