Bivariate Functional Normalization of Methylation Array Data

Abstract

DNA methylation plays a key role in disease analysis, especially for studies that compare known large scale differences in CpG sites, such as cancer/normal studies or between-tissues studies. However, before any analysis can be done, data normalization and preprocessing of methylation data are required. A useful data preprocessing pipeline for large scale comparisons is Functional Normalization (FunNorm), (Fortin et al., 2014) implemented in the minfi package in R. In FunNorm, the univariate quantiles of the methylated and unmethylated signal values in the raw data are used to preprocess the data. However, although FunNorm has been shown to outperform other preprocessing and data normalization processes for these types of studies, it does not account for the correlation between the methylated and unmethylated signals into account; the focus of this paper is to improve upon FunNorm by taking this correlation into account. The concept of a bivariate quantile is used in this study as an attempt to take the correlation between the methylated and unmethylated signals into consideration. From the bivariate quantiles found, the partial least squares method is then used on these quantiles in this preprocessing. The raw datasets used for this research were collected from the European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI) website. The results from this preprocessing algorithm were then compared and contrasted to the results from FunNorm. Drawbacks, limitations and future research are then discussed.