A statistical framework for Illumina DNA methylation arrays.

ABSTRACT:

Motivation

The Illumina BeadArray is a popular platform for profiling DNA methylation, an important epigenetic event associated with gene silencing and chromosomal instability. However, current approaches rely on an arbitrary detection P-value cutoff for excluding probes and samples from subsequent analysis as a quality control step, which results in missing observations and information loss. It is desirable to have an approach that incorporates the whole data, but accounts for the different quality of individual observations.

Results

We first investigate and propose a statistical framework for removing the source of biases in Illumina Methylation BeadArray based on several positive control samples. We then introduce a weighted model-based clustering called LumiWCluster for

SUBMITTER: Kuan PF 

PROVIDER: S-EPMC3025715 | biostudies-literature | 2010 Nov

REPOSITORIES: biostudies-literature