Handling missing DNA microarray data by kriging estimators

International Journal of Bioinformatics Research and Applications

Volumn 2, Issue 2, 2006, Pages 177-192

  Pham, Tuan D ^a,b  

^a JAMES COOK UNIVERSITY   (Australia)

^b School of Information Technology   (Australia)

Author keywords

Geostatistics; Kriging; Microarrays; Missing values

Indexed keywords

BRCA1 PROTEIN; BRCA2 PROTEIN; OLIGONUCLEOTIDE;

ACUTE GRANULOCYTIC LEUKEMIA; ACUTE LYMPHOBLASTIC LEUKEMIA; ARTICLE; B CELL LYMPHOMA; BREAST CANCER; CONTROLLED STUDY; CORRELATION COEFFICIENT; DNA MICROARRAY; GENE EXPRESSION; HUMAN; KRIGING; MATHEMATICAL COMPUTING;

EID: 33745864287     PISSN: 17445458     EISSN: 17445493     Source Type: Journal    
DOI: 10.1504/IJBRA.2006.009767     Document Type: Article

References (17)

1. Alizadeh, A.A., Eisen, M.B., Davis, R.E., Ma, C., Lossos, I.S., Rosenwald, A., Boldrick, J.C., Sabet, H., Tran, T., Yu, X., Powell, J.I., Yang, L., Marti, G.E., Moore, T., Hudson Jr., J., Lu, L., Lewis, D.B., Tibshirani, R., Sherlock, G., Chan, W.C., Greiner, T.C., Weisenburger, D.D., Armitage, J.O., Warnke, R., Levy, R., Wilson, W., Grever, M.R., Byrd, J.C., Botstein, D., Brown, P.O. and Staudt, L.M. (2000) 'Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling', Nature, Vol. 403, pp.503-511.
2. Bezdek, J.C. (1981) Pattern Recognition with Fuzzy Objective Function Algorithms, Plenum Press, New York.
3. Bø, T.H., Dysvik, B. and Jonassen, I. (2004) 'LSimpute: accurate estimation of missing values in microarray data with least squares methods', Nucleic Acids Research, Vol. 32, No. 3, p.34.
4. Cover, T.M. and Hart, P.E. (1967) 'Nearest neighbor pattern classification', IEEE Trans. Information Theory, Vol. 13, pp.21-27.
5. David, M. (1977) Geostatistical Ore Reserve Estimation, Elsevier, Amsterdam.
6. Duda, R. and Hart, P. (1973) Pattern Classification and Scene Analysis, John Wiley & Sons, New York.
7. Golub, T.R., Slonim, D.K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov, P., Coller, H., Loh, M.L., Downing, J.R., Caligiuri, M.A., Bloomfield, C.D. and Lander, E.S. (1999) 'Molecular classification of cancer: class discovery and class prediction by gene expression monitoring', Science, Vol. 286, pp.531-537.
8. Hedenfalk, I., Duggan, D., Chen, Y., Radmacher, M., Bittner, M., Simon, R., Meltzer, P., Gusterson, B., Esteller, M., Kallioniemi, O., Wilfond, B., Borg, A. and Trent, J. (2001) 'Gene-expression profiles in hereditary breast cancer', The New England Journal of Medicine, Vol. 344, pp.539-548.
9. Isaaks, E.H. and Srivastava, R.M. (1989) An Introduction to Applied Geostatistics, Oxford University Press, New York.
10. Journel, A.G. and Huibregts, C.J. (1978) Mining Geo Statistics, Academic Press, London.
11. Journel, A.G. and Rao, S.E. (1996) 'Deriving conditional distribution from ordinary kriging', Stanford Center for Reservoir Forcasting, Stanford University Report No. 29, p.25.
12. Kellam, P. and Liu, X. (2003) 'Experimental use of DNA arrays', in Orengo, C.A., Jones, D.T. and Thornton, J.M. (Eds.): Bioinformatics: Genes, Proteins and Computers, Bios, Oxford, UK.
13. Kim, H., Golub, G.H. and Park, H. (2005) 'Missing value estimation for DNA microarray gene expression data: local least squares imputation', Bioinformatics, Vol. 21, pp.187-198.
14. Krane, D.E. and Raymer, M.L. (2003) Fundamental Concepts of Bioinformatics, Benjamin Cummings, San Francisco, CA, USA.
15. Nguyen, D.V., Wang, N. and Carroll, R.J. (2004) 'Evaluation of missing value estimation for microarray data'. Journal of Data Science, Vol. 2, pp.347-370.
16. Oba, S., Sata, M., Takesama, L, Monden, M., Matsubara, K. and Ishii, S. (2003) 'A Bayesian missing value estimation method for gene expression profile data', Bioinformatics, Vol. 19, pp.2088-2096.
17. Troyanskaya, O., Cantor, M., Sherlock, G., Brown, P., Hastie, T., Tibshirani, R., Bostein, D. and Altman, R.B. (2001) 'Missing value estimation methods for DNA microarrays', Bioinformatics, Vol. 17, pp.520-525.