Robust Image Analysis of BeadChip Microarrays

Jan Kalina, Anna Schlenker


Microarray images in molecular genetics are heavily contaminated by noise and outlying measurements. This paper is devoted to analysis of Illumina BeadChip microarray images, primarily to their low-level preprocessing. We point out that standard image analysis procedures, which are implemented in the beadarray package of BioConductor software, are highly sensitive to contamination by severe noise and outliers. Therefore, the habitually used methodology does not discover many of the outliers. We illustrate this on real data and show that the standard background correction method may actually amplify the noise in the image. A robust image analysis tailor-made for this type of microarray images is highly desirable. We explain principles and show preliminary results of our robust alternative to the standard approach, which aims to be robust to noise and outliers in each its step.


  1. Cardona, A. and Tomancak, P. (2012). Current challenges in open-source bioimage informatics. Nature Methods, 9:661-665.
  2. Davies, P. and Gather, U. (2005). Breakdown and groups. Annals of Statistics, 33:997-1035.
  3. Dunning, M., Barbosa-Morais, N., Lynch, A., Tavaré, S., and Ritchie, M. (2008). Statistical issues in the analysis of Illumina data. BMC Bioinformatics, 9(85).
  4. Dunning, M., M.L. Smith, M. R., and Tavaré, S. (2007). Beadarray: R classes and methods for Illumina beadbased data. Bioinformatics, 23:2183-2184.
  5. Filzmoser, P. and Todorov, V. (2011). Review of robust multivariate statistical methods in high dimension. Analytica Chinica Acta, 705:2-14.
  6. Fraser, K., Wang, Z., and Liu, X. (2010). Microarray image analysis: An algorithmic approach. Chapman & Hall/CRC, Boca Raton.
  7. Göhlmann, H. and Talloen, W. (2009). Gene expression studies using Affymetrix microarrays. Chapman & Hall/CRC, Boca Raton.
  8. Kalina, J. (2012). Implicitly weighted methods in robust image analysis. Journal of Mathematical Imaging and Vision, 44:449-462.
  9. Kalina, J. (2014). Classification analysis methods for high-dimensional genetic data. Biocybernetics and Biomedical Engineering, 34:10-18.
  10. Kalina, J. and Zvárová, J. (2013). Decision support systems in the process of improving patient safety. In E-health Technologies and Improving Patient Safety: Exploring Organizational Factors. IGI Global, Hershey, 71-83.
  11. Kuhn, K., Baker, S., Chudin, E., Lieu, M.-H., Oeser, S., Bennett, H., Rigault, P., Barker, D., McDaniel, T., and Chee, M. (2004). A novel, high-performance random array platform for quantitative gene expression profiling. Genome Research, 14:2347-2356.
  12. Rueda, L. (2014). Microarray image and data analysis: Theory and practice. CRC Press, Boca Raton.
  13. Shi, W., Banerjee, A., Ritchie, M., Gerondakis, S., and Smyth, G. (2009). Illumina WG-6 beadchip strips should be normalized separately. BMC Bioinformatics, 10(372).
  14. Smith, M., Dunning, M., Tavaré, S., and Lynch, A. (2010). Identification and correction of previously reported spatial phenomena using raw Illumina BeadArray data. BMC Bioinformatics, 11(208).
  15. Tanaka, G., Suetake, N., and Uchino, E. (2010). Image enhancement based on nonlinear smoothing and sharpening for noisy images. Journal of Advanced Computational Intelligence and Intelligent Informatics, 14:200-207.
  16. Tibshirani, R., Hastie, T., and Narasimhan, B. (2003). Class prediction by nearest shrunken centroids, with applications to dna microarrays. Statistical Science, 18:104-117.
  17. Xanthopoulos, P., Pardalos, P., and Trafalis, T. (2013). Robust data mining. Springer, New York.

Paper Citation

in Harvard Style

Kalina J. and Schlenker A. (2015). Robust Image Analysis of BeadChip Microarrays . In Proceedings of the International Conference on Bioimaging - Volume 1: BIOIMAGING, (BIOSTEC 2015) ISBN 978-989-758-072-7, pages 89-94. DOI: 10.5220/0005246900890094

in Bibtex Style

author={Jan Kalina and Anna Schlenker},
title={Robust Image Analysis of BeadChip Microarrays},
booktitle={Proceedings of the International Conference on Bioimaging - Volume 1: BIOIMAGING, (BIOSTEC 2015)},

in EndNote Style

JO - Proceedings of the International Conference on Bioimaging - Volume 1: BIOIMAGING, (BIOSTEC 2015)
TI - Robust Image Analysis of BeadChip Microarrays
SN - 978-989-758-072-7
AU - Kalina J.
AU - Schlenker A.
PY - 2015
SP - 89
EP - 94
DO - 10.5220/0005246900890094