preprocessing differential methylation hybridization microarray data预处理差异甲基化杂化微阵列数据.pdf

Sun et al. BioData Mining 2011, 4:13 /content/4/1/13 BioData Mining METHODOLOGY Open Access Preprocessing differential methylation hybridization microarray data 1,2* 3 3 3 4 Shuying Sun , Yi-Wen Huang , Pearlly S Yan , Tim HM Huang and Shili Lin * Correspondence: Abstract ssun5211@ 1Case Comprehensive Cancer Background: DNA methylation plays a very important role in the silencing of tumor Center, Case Western Reserve University, Cleveland, Ohio, 44106, suppressor genes in various tumor types. In order to gain a genome-wide USA understanding of how changes in methylation affect tumor growth, the differential Full list of author information is methylation hybridization (DMH) protocol has been developed and large amounts of available at the end of the article DMH microarray data have been generated. However, it is still unclear how to preprocess this type of microarray data and how different background correction and normalization methods used for two-color gene expression arrays perform for the methylation microarray data. In this paper, we demonstrate our discovery of a set of internal control probes that have log ratios (M) theoretically equal to zero according to this DMH protocol. With the aid of this set of control probes, we propose two LOESS (or LOWESS, locally weighted scatter-plot smoothing) normalizatio