Determination of minimum sample size and discriminatory expression patterns in microarray data

Bioinformatics

Volumn 18, Issue 9, 2002, Pages 1184-1193

  Hwang, Daehee ^a   Schmitt, William A ^a   Stephanopoulos, George ^a   Stephanopoulos, Gregory ^a  

^a Massachusetts Institute of Technology Cambridge   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ACUTE LEUKEMIA; ALGORITHM; ARTICLE; CALCULATION; DNA MICROARRAY; FISHER DISCRIMINANT ANALYSIS; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC TRANSCRIPTION; PHENOTYPIC VARIATION; POWER ANALYSIS; PRIORITY JOURNAL; RELIABILITY; SAMPLE SIZE; STATISTICAL ANALYSIS;

MARTES PENNANTI;

EID: 0036738906     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/18.9.1184     Document Type: Article

References (27)

1. Alizadeh,A.A. et al. (2000) Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature, 403, 503-511.
2. Alter,O., Brown,P.O. and Botstein,D. (2000) Singular value decomposition for genome-wide expression data processing and modeling. Proc. Natl Acad. Sci. USA, 97, 10101-10106.
3. Cohen,J. (1988) Statistical power analysis for the behavioral sciences, 2nd edn, Erlbaum, Hillsdale, NJ.
4. Dillon,W.R. and Goldstein,M. (1984) Multivariate Analysis. Wiley, New York.
5. Dudoit,S. et al. (2001) Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statistica Sinica (to appear), UC Berkeley Statistics Technical Report.
6. Dudoit,S., Fridlyand,J. and Speed,T.P. (2000) Comparison of discrimination methods for the classification of tumors using gene expression data. J. Amer. Stat. Assoc. (to appear), Technical Report 576.
7. power reference material. http://www.psycho.uni-duesseldorf. de/aap/projects/gpower/reference/referencen̄ual. html#noncentral.
8. Golub,T.R. et al. (1999) Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science, 286, 531-537.
9. Holter,N.S. et al. (2000) Fundamental patterns underlying gene expression profiles: Simplicity from complexity. Proc. Natl Acad. Sci. USA, 97, 8409-8414.
10. Johnson,R.A. and Wichern,D.W. (1992) Applied Multivariate Statistical Analysis. Prentice Hall, New Jersey.
11. Kraemer,H.C. and Thiemann,S. (1987) How Many Subjects? Statistical Power Analysis in Research. Sage, Newbury Park, CA.
12. Lachenbruch,P.A. and Mickey,M.R. (1968) Estimation of error rates in discriminant analysis. Technometrics, 10, 1-11.
13. Lockhart,D.J. et al. (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol., 14, 1675-1680.
14. Mace,A.E. (1974) Sample-size determination. Krieger, Huntington, NY.
15. Olson,C.L. (1974) Comparative robustness of six tests in multivariate analysis of variance. J. Amer. Stat. Assoc., 69, 894-908.
16. Other F-tests. http://www.psycho.uni-duesseldorf.de/aap/projects/ gpower/reference/referencen̄ual.html#t3.
17. Pan,W., Lin,J. and Le,C. (2001) How many replicates of arrays are required to detect gene expression changes in microarray experiments? A mixture model approach. Biostatistics, University of MN Technnical Report.
18. SAS/STAT User's Guide (1989) 4th edn, SAS Institute, Cray, NC.
19. Schena,M., Shalon,D., Davis,R.W. and Brown,P.O. (1995) Quantitative monitoring of gene-expression patterns with a complementary-DNA microarray. Science, 270, 467-470.
20. Stephanopoulos,G. et al. (2002) Mapping Physiological States from Microarray Expression Measurements. Bioinformatics, in Press.
21. Storey,J.D. and Tibshirani,R. (2001) Estimating false discovery rates under dependence with applications to DNA microarrays, Stanford Technical Report.
22. Thall,P.F.E (1995) Recent Advances in Clinical Trial Design and Analysis. Kluwer, Boston.
23. Thomas,J. et al. (2001) An efficient and robust statistical modeling approach to discover diffentially expressed genes using genomic expression profiles. Genome Res., 11, 1227-1236.
24. Tusher,VG., Tibshirani,R. and Chu,G. (2001) Significance analysis of microarrays applied to the ionizing radiation response. PNAS, 98, 5116-5121.
25. West,M. et al. (2001) DNA microarray data analysis and regression modeling for genetic expression profiling. CAMDA.
26. Zhao,G. and Maclean,A.L. (2000) A comparison of canonical discriminant analysis and principal component analysis for spectral transformation. Photogramm Eng. Rem. S, 66, 841-847.
27. Zien,A. et al. (2001) Microarrays: How many do you need? Proceedings of the Sixth Annual International Conference on Computational Biology. RECOMB.