A Robust Pre-processing of BeadChip Microarray Images

0489959 - ÚI 2019 RIV PL eng J - Journal Article
Kalina, Jan
A Robust Pre-processing of BeadChip Microarray Images.
Biocybernetics and Biomedical Engineering. Roč. 38, č. 3 (2018), s. 556-563. ISSN 0208-5216. E-ISSN 0208-5216
Institutional support: RVO:67985807
Keywords : Microarray * Robust image analysis * Noise * Outlying measurements * Background effect
OECD category: Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
Impact factor: 2.159, year: 2018

Microarray images commonly used in gene expression studies are heavily contaminated by noise and/or outlying values (outliers). Unfortunately, standard methodology for the analysis of Illumina BeadChip microarray images turns out to be too vulnerable to data contamination by outliers. In this paper, an alternative approach to low-level pre-processing of images obtained by the BeadChip microarray technology is proposed. The novel approach robustifies the standard methodology in a complex way and thus ensures a sufficient robustness (resistance) to outliers. A gene expression data set from a cardiovascular genetic study is analyzed and the performance of the novel robust approach is compared with the standard methodology. The robust approach is able to detect and delete a larger percentage of outliers. More importantly, gene expressions are estimated more precisely. As a consequence, also the performance of a subsequently performed classification task to two groups (patients vs. control persons) is improved over the cardiovascular gene expression data set. A further improvement was obtained when considering weighted gene expression values, where the weights correspond to a robust estimate of variability of the measurements for each individual gene transcript.
Permanent Link: http://hdl.handle.net/11104/0284252