Evaluating the effect of various background correction methods regarding noise reduction, in two-channel microarray data

Abstract In this work, two novel background correction (BC) methods, along with several commonly used ones, are evaluated regarding noise reduction in eleven two-channel self-versus-self (SVS) hybridizations. The evaluation of each BC method is investigated under the use of four statistical criteria...

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Veröffentlicht in:	Computers in biology and medicine 2012-01, Vol.42 (1), p.19-29
Hauptverfasser:	Sifakis, E.G, Prentza, A, Koutsouris, D, Chatziioannou, A.A
Format:	Artikel
Sprache:	eng
Schlagworte:	Animals Arabidopsis - genetics Background estimation Computational Biology - methods Computer applications Data Interpretation, Statistical Databases, Genetic Deoxyribonucleic acid DNA DNA microarrays Dyes Estimates Experiments Gene expression Gene Expression Profiling - methods Humans Hybridization Internal Medicine Mean square errors Methods Mice Normalization techniques Oligonucleotide Array Sequence Analysis - methods Other Self-versus-self hybridizations Studies Transcriptomic analysis
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Zusammenfassung:	Abstract In this work, two novel background correction (BC) methods, along with several commonly used ones, are evaluated regarding noise reduction in eleven two-channel self-versus-self (SVS) hybridizations. The evaluation of each BC method is investigated under the use of four statistical criteria combined into a single measure, the polygon area measure. Overall, our proposed BC approaches perform very well in terms of the proposed measure for most of the cases and provide an improved effect regarding technical noise reduction.
ISSN:	0010-4825 1879-0534
DOI:	10.1016/j.compbiomed.2011.10.003