Summary
Microarrays allow the simultaneous measurement of the expression levels of thousands of genes. This unique data structure has inspired a completely new area of research in statistics and bioinformatics. The objective of the present chapter is to review some of the main statistical tools used in this context. We will mainly focus on low-level preprocessing steps: image analysis, data transformation, normalization, and multiple testing for differential expression. The high-level inference of genetic regulatory interactions from preprocessed microarray data will be covered in Chapters 8 and 9.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
O. Alter, P. Brown, and D. Botstein. Singular value decomposition for genome-wide expression data processing and modeling. Proceedings of the National Academy of Sciences of the USA, 97:10101–6, 2000.
Axon Instruments, Inc. GenePix 400A User’s Guide. 1999.
P. Baldi and W. Hatfield. DNA Microarrays and Gene Expression. Cambridge University Press, 2002.
P. Baldi and A. Long. A Bayesian framework for the analysis of microarray expression data: Regularized t-test and statistical inferences of gene changes. Bioinformatics, 17:509–519, 2001.
B. Bolstad, R. A. Irizarry, M. Astrand, and T. Speed. A comparison of normalization methods for high density oligonucleotide array data based on bias and variance. Bioinformatics, 19(2):185–193, 2002.
D. Bozinov and J. Rahnenführer. Unsupervised technique for robust target separation and analysis of microarray spots through adaptive pixel clustering. Bioinformatics, 18:747–756, 2002.
N. Brändle, H.-Y. Chen, H. Bischof, and H. Lapp. Robust parametric and semi-parametric spot fitting for spot array images. In ISMB’00 — 8th International Conference on Intelligent Systems for Molecular Biology, pages 46–56, 2000.
C. S. Brown, P. C. Goodwin, and P. K. Sorger. Image metrics in the statistical analysis of DNA microarray data. Proceedings of the National Academy of Sciences of the USA, 98:8944–8949, 2001.
Y. Chen, E. Dougherty, and M. Bittner. Ratio-based decisions and the quantative analysis of cDNA microarray images. Journal of Biomedical Optics, 2:364–374, 1997.
H. Chipman, T. Hastie, and R. Tibshirani. Clustering microarray data. In T. Speed, editor, Statistical Analysis of Gene Expression Microarray Data, pages 159–200. Chapman & Hall/CRC, 2003.
X. Cui, M. Kerr, and G. Churchill. Transformations for cDNA microarray data. Statistical Applications in Genetics and Molecular Biology, 2, 2003.
S. Dudoit and J. Fridlyand. Classification in microarray experiments. In T. Speed, editor, Statistical Analysis of Gene Expression Microarray Data, pages 93–158. Chapman & Hall/CRC, 2003.
S. Dudoit, Y. Yang, M. Callow, and T. Speed. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Technical Report 578, Statistics Dept, UC Berkeley, 2000.
B. Durbin, J. Hardin, D. Hawkins, and D. Rocke. A variance-stabilizing transformation for gene-expression microarray data. Bioinformatics, 18:105–110, 2002.
B. Efron, R. Tibshirani, J. Storey, and V. Tusher. Empirical Bayes analysis of a microarray experiment. Journal of the American Statistical Association, 96:1151–1160, 2001.
M. B. Eisen. ScanAlyse. 1999. (Available at http://rana/Stanford.EDU/∼software/)
Y. Ge, S. Dudoit, and T. Speed. Resampling-based multiple testing for microarray data analysis. Technical Report 633, Statistics Dept, UC Berkeley, 2003.
C. A. Glasbey and P. Ghazal. Combinatorial image analysis of DNA microarray features. Bioinformatics, 19:194–203, 2003.
C. A. Glasbey and G. W. Horgan. Image Analysis for the Biological Sciences. Wiley, Chichester, 1995.
T. Golub, D. Slonim, P. Tamayo, C. Huard, M. Gaasenbeek, J. Mesirov, H. Coller, M. Loh, J. Downing, M. Caligiuri, C. Bloomfield, and E. Lander. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science, 286:531–537, 1999.
GSI Luminomics. QuantArray Analysis Software, Operator’s Manual. 1999.
D. Hoyle, M. Rattray, R. Jupp, and A. Brass. Making sense of microarray data distributions. Bioinformatics, 18:576–584, 2002.
W. Huber, A. von Heydebreck, H. Sültmann, A. Proustka, and M. Vingron. Variance stabilization applied to microarray data calibration and to quantification of differential expression. Bioinformatics, 18:96–104, 2002.
W. Huber, A. von Heydebreck, and M. Vingron. Analysis of microarray gene expression data. In Handbook of Statistical Genetics. Wiley, second edition, 2003.
R. Irizarry, B. Bolstad, F. Collin, L. Cope, B. Hobbs, and T. Speed. Summaries of affymetrix genechip probe level data. Nucleic Acids Research, 31:e 15, 2003.
A. N. Jain, T. A. Tokuyasu, A. M. Snijders, R. Segraves, D. G. Albertson, and D. Pinkel. Fully automatic quantification of microarray image data. Genome Research, 12:325–332, 2002.
A. Janssen. Studentized permutation tests for non i.i.d. hypotheses and the generalized Behrens-Fisher problem. Statististics and Probability Letters, 36:9–21, 1997.
M. Kerr and G. Churchill. Experimental design for gene expression microarrays. Biostatistics, 2:183–201, 2001.
M. Kerr, M. Martin, and G. Churchill. Analysis of variance for gene expression microarray data. Journal of Computational Biology, 7:819–837, 2000.
J. H. Kim, H. Y. Kim, and Y. S. Lee. A novel method using edge detection for signal extraction from cDNA microarray image analysis. Experimental and Molecular Medicine, 33:83–88, 2001.
M. Lee, F. Kuo, G. Whitmore, and J. Sklar. Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetetive cDNA hybridizations. Proceedings of the National Academy of Sciences of the USA, 97:9834–9839, 2000.
M. Newton, C. Kendziorski, C. Richmond, F. Blattner, and K. Tsui. On differential variability of expression ratios: Improving statistical inference about gene expression changes from microarray data. Journal of Computational Biology, 8:37–52, 2000.
NHGRI. Image processing software tools. 2003. (Available at http://www.nhgri.nih.gov/DIR/LCG/15K/HTML/img_analysis.html)
G. Parmigiani, E. S. Garrett, R. Irizarry, and S. Zeger, editors. The Analysis of Gene Expression Data. Springer, 2003.
D. Rocke and B. Durbin. A model for measurement error for gene expression arrays. Journal of Computational Biology, 8:557–569, 2001.
M. Rudemo, T. Lobovkin, P. Mostad, S. Scheidl, S. Nilsson, and P. Lindahl. Variance models for microarray data. Technical report, Mathematical Statistics, Chalmers University of Technology, 2002.
E. Schadt, C. Li, B. Eliss, and W. Wong. Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. Journal of Cellular Biochemistry, 84:120–125, 2002.
T. Speed, editor. Statistical Analysis of Gene Expression Microarray Data. Chapman & Hall/CRC, 2003.
M. Steinfath, W. Wruck, H. Seidel, H. Lehrach, U. Radelof, and J. O’Brien. Automated image analysis for array hybridization experiments. Bioinformatics, 17:634–641, 2001.
J. Storey. False Discovery Rates: Theory and Applications to DNA Microarrays. PhD thesis, Department of Statistics, Stanford University, 2002.
V. Tusher, R. Tibshirani, and G. Chu. Significance analysis of microarrays applied to the ionizing radiation response. Proceedings of the National Academy of Sciences of the USA, 98:5116–5121, 2001.
L. Wernisch, S. Kendall, S. Soneji, A. Wietzorrek, T. Parish, J. Hinds, P. Butcher, and N. Stoker. Analysis of whole-genome microarray replicates using mixed models. Bioinformatics, 19:53–61, 2003.
P. Westfall and S. Young. Resampling-based multiple testing: examples and methods for p-value adjustment. Wiley series in probability and mathematical statistics. Wiley, 1993.
R. Wolfinger, G. Gibson, E. Wolfinger, L. Bennett, H. Hamadeh, P. Bushel, C. Afshari, and R. Paules. Assessing gene significance from cDNA microarray expression data via mixed models. Journal of Computational Biology, 8(6):625–637, 2001.
Y. Yang, S. Dudoit, P. Luu, D. Lin, V. Peng, J. Ngai, and T. Speed. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research, 30(4):e 15, 2002.
Y. Yang, S. Dudoit, P. Luu, and T. Speed. Normalization for cDNA microarray data. In M. Bittner, Y. Chen, A. Dorsel, and E. Dougherty, editors, Microarrays: Optical Technologies and Informatics, volume 4266 of Proceedings of SPIE, 2001.
Y. H. Yang, M. J. Buckley, S. Dudoit, and T. P. Speed. Comparison of methods for image analysis on cDNA microarray data. Journal of Computational and Graphical Statistics, 11:108–136, 2002.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag London Limited
About this chapter
Cite this chapter
Mayer, CD., Glasbey, C.A. (2005). Statistical Methods in Microarray Gene Expression Data Analysis. In: Husmeier, D., Dybowski, R., Roberts, S. (eds) Probabilistic Modeling in Bioinformatics and Medical Informatics. Advanced Information and Knowledge Processing. Springer, London. https://doi.org/10.1007/1-84628-119-9_7
Download citation
DOI: https://doi.org/10.1007/1-84628-119-9_7
Publisher Name: Springer, London
Print ISBN: 978-1-85233-778-0
Online ISBN: 978-1-84628-119-8
eBook Packages: Computer ScienceComputer Science (R0)