A Robust Pre-processing of BeadChip Microarray Images

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F67985807%3A_____%2F18%3A00489959" target="_blank" >RIV/67985807:_____/18:00489959 - isvavai.cz</a>
Result on the web
<a href="http://dx.doi.org/10.1016/j.bbe.2018.04.005" target="_blank" >http://dx.doi.org/10.1016/j.bbe.2018.04.005</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1016/j.bbe.2018.04.005" target="_blank" >10.1016/j.bbe.2018.04.005</a>

Result language
angličtina
Original language name
A Robust Pre-processing of BeadChip Microarray Images
Original language description
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.
Czech name
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Czech description
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Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project
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Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year
2018
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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