Microarray Image Processing and Quality Control

  • Anton Petrov
  • Soheil Shams


Image processing is an important stage of every microarray experiment. Reliability of this stage strongly influences the results of data analysis performed on extracted gene expressions. Multiple methods related to array recognition, spot segmentation and measurement extraction have emerged in this area over past several years. Currently there are various commercial and freeware packages available, which perform microarray image analysis. This paper attempts to review microarray image analysis as a whole and to make some experimental comparison of several computational schemes for signal segmentation and measurement extraction. Also we provide a detailed discussion of automated image quality control for use with microarray images.

microarray image processing image segmentation microarray quality control microarray batch automation cDNA microarrays 


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  1. 1.
    D.E. Bassett, M.B. Eisen, and M.S. Boguski, “Gene Expression Informatics—It's all in Your Mine,” Nature Genetics Supplement, 1999, p. 21, 48.Google Scholar
  2. 2.
    Y-X. Zhou, P. Kalocsai, J.-Y. Chen, and S. Shams, “Information Processing Issues and Solutions Associated with Microarray Technology,” in Microarray Biochip Technology, Schena (Ed.), Eaton Publishing, Massachusetts, 2000, pp. 167–200.Google Scholar
  3. 3.
    L.J. Heyer, S. Kruglyak, and S. Yooseph, “Exploring Expression Data: Identification and Analysis of Coexpressed Genes,” Genome Research, vol. 9, 1999, p. 1106.CrossRefGoogle Scholar
  4. 4.
    Y.H. Yang, M.J. Buckley, S. Dudoit, and T.P. Speed, “Comparison of Methods for Image Analysis on cDNA Microarray Data,” Technical report, no. 584, Department of Statistics, University of California, Berkeley, 2000.Google Scholar
  5. 5.
    D. Bozinov and J. Rahnenf¨ uhrer, “Unsupervised Technique for Robust Target Separation and Analysis of Microarray Spots through Adaptive Pixel Clustering,” Bioinformatics, vol. 18, 2002, pp. 747–756.CrossRefGoogle Scholar
  6. 6.
    R.A. Johnson and D.A. Wichern, Applied Multivariate Statistical Analysis. N.J.: Prentice Hall, 1998.Google Scholar
  7. 7.
    S.G. Hilsenbeck, W.E. Friedrichs, R. Schiff, P. O'Connell, R.K. Hansen, C.K. Osborne, and S.A.W. Fuqua, “Statistical Analysis of Array Expression Data as Applied to the Problem of Tamoxifen resistance,” Journal of the National Cancer Institute, vol. 91, 1999, p. 453.CrossRefGoogle Scholar
  8. 8.
    Y. Chen, E.R. Dougherty, and M.L. Bittner, “Ratio-Based Decisions and the Quantitative Analysis of cDNA Microarray Images,” Journal of Biomedical Optics, vol. 2, no. 4, 1997.Google Scholar
  9. 9.
    R.O. Duda and P.E. Hart, Pattern Classification and Scene Analysis. J. Wiley, 1973.Google Scholar
  10. 10.
    R. Adams and L. Bischof, “Seeded Region Growing,” IEEE Transactions on Pattern Analysis and Machine Intelligence, no. 16, 1994.Google Scholar
  11. 11.
    K.R. Castleman, Digital Image Processing. Prentice Hall, 1996.Google Scholar
  12. 12.
    J. Brody, B. Williams, B. Wol, and S. Quake, “Significance and Statistical Errors in the Analysis of DNA Microarray Data,” PNAS, vol. 99, no. 20, 2002, pp. 12975–12978.CrossRefGoogle Scholar
  13. 13.
    M.-L.T. Lee, F.C. Kuo, G.A. Whitmore, and J. Sklar, “Importance of Replication in Microarray Gene Expression Studies: Statistical Methods and Evidence from Repetitive cDNA Hybridizations,” PNAS,vol. 97, no. 18, 2000.Google Scholar
  14. 14.
    G.C. Tseng, M.K. Oh, L. Rohlin, J.C. Liao, and W.H. Wong, Issues in cDNAMicroarray Analysis: Quality Filtering, Channel Normalization, Models of Variations and Assessment of Gene Effects,” Nucleic Acids Res, vol. 29, 2001, pp. 2549–2557.CrossRefzbMATHGoogle Scholar
  15. 15.
    D.M. Mutch, A. Berger, R. Mansourian, A. Rytz, and M.A. Roberts, “The Limit Fold Change Model: A Practical Approach for Selecting Differentially Expressed Genes from Microarray Data,” BMC Bioinformatics, vol. 3, no. 17, 2002.Google Scholar

Copyright information

© Kluwer Academic Publishers 2004

Authors and Affiliations

  • Anton Petrov
    • 1
  • Soheil Shams
    • 1
  1. 1.BioDiscovery Inc.

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