Pixel-level signal modelling with spatial correlation for two-colour microarrays

Statistical Applications in Genetics and Molecular Biology

Volumn 4, Issue 1, 2005, Pages

  Ekstrøm, Claus T ^a   Bak, Søren ^a   Rudemo, Mats ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Censored data; Polynomial hyperbolic model; Spatial correlation; Spotted array

Indexed keywords

ARABIDOPSIS; ARTICLE; CORRELATION ANALYSIS; DATA ANALYSIS; DNA MICROARRAY; GENETIC ANALYSIS; IMAGE ANALYSIS; LASER MICROSCOPY; NORMAL DISTRIBUTION; STATISTICAL ANALYSIS; STATISTICAL MODEL;

EID: 84860945403     PISSN: 15446115     EISSN: 15446115     Source Type: Journal    
DOI: 10.2202/1544-6115.1112     Document Type: Article

References (11)

1. Bak, S., Olsen, C. E., Halkier, B. A., and Møller, B. L. (2000). Transgenic tobacco and arabidopsis plants expressing the two multifunctional sorghum cytochromes P450, CYP79A1 and CYP71E1, are cyanogenic and accumulate metabolites derived from intermediates in dhurrin biosynthesis. Plant Physiology, 123:1437-1448.
2. Bak, S., Olsen, C. E., Petersen, B. L., Møller, B. L., and Halkier, B. A. (1999). Metabolic engineering of p-hydroxybenzylglucosinolate in Arabidopsis by expression of the cyanogenic CYP79A1 from Sorghum bicolor. Plant Journal, 20:663-672.
3. Box, G. E. P. and Cox, D. R. (1964). An analysis of transformations. Journal of the Royal Statistical Society, Series B, 26:211-252.
4. Cressie, N. (1993). Statistics for Spatial Data, revised edition. Wiley.
5. Dempster, A. P., Laird, N. M., and Rubin, D. B. (1977). Maximum likelihood from incomplete data via the EM algorithm. Journal Royal Statistical Society, Series B, 39:1-38.
6. Ekstrøm, C. T., Kristensen, C., Bak, S., and Rudemo, M. (2004). Spot shape modelling and data transformations for microarrays. Bioinformatics, 20:2270-2278.
7. Kane, M. D., Jatkoe, T. A., Stumpf, C. R., Lu, J., Thomas, J. D., and Madore, S. J. (2000). Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Research, 28:4552-4557.
8. Kristensen, C., Morant, M., Olsen, C. E., Ekstrøm, C. T., Galbraith, D. W., Møller, B. L., and Bak, S. (2005). Metabolic engineering of dhurrin in transgenic Arabidopsis plants with marginal inadvertent effects on the metabolome and transcriptome. PNAS, 102:1779-1784.
9. Pinheiro, J. C. and Bates, D. M. (2000). Mixed-Effects Models in S and S-PLUS. Springer, New York, USA.
10. Tattersall, D. B., Bak, S., Jones, P. R., Olsen, C. E., Nielsen, J. K., Hansen, M. K., Høj, P. B., and Møller, B. L. (2001). Resistance to an herbivore through engineered cyanogenic glucoside synthesis. Science, 293:1826-1828.
11. Wierling, C. K., Steinfach, M., Elge, T., Schulze-Kremer, S., Aanstad, P., Clark, M., Lehrach, H., and Herwig, R. (2002). Simulation of dna array hybridization experiments and evaluation of critical parameters during subsequent image and data analysis. BMC Bioinformatics, 3:29.