Abstract
It is well known that microarray printing, hybridization, and washing oftentimes create erroneous measurements, and these errors detrimentally impact machine microarray spot quality classification. Thus, it is crucial to identify and remove these errors if automation is to replace the still common practice of visually assessing spot quality, an extremely expensive and time-consuming procedure. A major problem in microarray spot quality classification methods proposed in the literature is the correlation among the features extracted from the spots. In this paper, we propose using a random subspace ensemble of neural networks and a feature selection algorithm to improve the performance of our microarray spot quality classification method. Our best method obtains an error under the receiver operating characteristic curve (EAUR) of 0.3 outperforming the stand-alone support vector machine EAUR of 1.7. The consistency of our proposed approach makes it a viable alternative to the labour-intensive manual method of spot quality assessment.
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Implemented as in the Matlab PRTools 3.1.7.
Cy3 and Cy5 are reactive water-soluble fluorescent dyes of the cyanine dye family. Cy3 dyes are green (~550 nm excitation, ~570 nm emission), while Cy5 is fluorescent in the red region (~650/670 nm). For details, see http://www.jacksonimmuno.com/technical/f-cy3-5.asp.
These parameters are found with a grid search to minimize the EAUR.
Implemented as in OSU SVM Matlab Toolbox.
Radial basis function: exp(−gamma ||a–b||2).
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The authors would like to thank S. Hautaniemi for sharing the data set.
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Nanni, L., Lumini, A. & Brahnam, S. Advanced machine learning techniques for microarray spot quality classification. Neural Comput & Applic 19, 471–475 (2010). https://doi.org/10.1007/s00521-010-0342-3
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DOI: https://doi.org/10.1007/s00521-010-0342-3