title: A comparison of normalization techniques for microRNA microarray data.
abstract: Normalization of expression levels applied to microarray data can help in reducing measurement error. Different methods, including cyclic loess, quantile normalization and median or mean normalization, have been utilized to normalize microarray data. Although there is considerable literature regarding normalization techniques for mRNA microarray data, there are no publications comparing normalization techniques for microRNA (miRNA) microarray data, which are subject to similar sources of measurement error. In this paper, we compare the performance of cyclic loess, quantile normalization, median normalization and no normalization for a single-color microRNA microarray dataset. We show that the quantile normalization method works best in reducing differences in miRNA expression values for replicate tissue samples. By showing that the total mean squared error are lowest across almost all 36 investigated tissue samples, we are assured that the bias correction provided by quantile normalization is not outweighed by additional error variance that can arise from a more complex normalization method. Furthermore, we show that quantile normalization does not achieve these results by compression of scale.
authors.affiliation: The Ohio State University, USA. rao@stat.ohio-state.edu
authors.forename: Youlan
authors.initials: Y
authors.lastname: Rao
authors.forename: Yoonkyung
authors.initials: Y
authors.lastname: Lee
authors.forename: David
authors.initials: D
authors.lastname: Jarjoura
authors.forename: Amy S
authors.initials: AS
authors.lastname: Ruppert
authors.forename: Chang-Gong
authors.initials: CG
authors.lastname: Liu
authors.forename: Jason C
authors.initials: JC
authors.lastname: Hsu
authors.forename: John P
authors.initials: JP
authors.lastname: Hagan
mesh_terms: D000465:Algorithms; D000818:Animals; D015982:Bias; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000032:analysis* / Q000235:genetics; D015233:Models, Statistical; D016011:Normal Distribution; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data*; D012334:RNA, Neoplasm / Q000032:analysis / Q000235:genetics; D015203:Reproducibility of Results; D012107:Research Design
chemical_list: D035683:MicroRNAs; D012334:RNA, Neoplasm