In preprint:

Jean-Philippe Fortin, Aurelie Labbe, Mathieu Lemire, Brent W. Zanke, Thomas J. Hudson, Elana J. Fertig, Celia M.T. Greenwood, Kasper D. Hansen Functional normalization of 450k methylation array improves replication in cancer studies
bioRxivdoi: 10.1101/002956

I have developed a between-array normalization method for methylation data, called Functional Normalization (FunNorm) , which is an extension of quantile normalization to handle covariates known to be associated with unwanted variation. We have adapted functional normalization to the Illumina Human 450K methylation array, and the method is available as the preprocessFunnorm function in the development version of minfi .

I am also developing an interactive visualization package for the Illumina Infinium 450k array, called shinyMethyl, available for download here .

During the Bioconductor Conference 2013, I gave a workshop about how to combine the packages minfi and shinyMethyl to analyze methylation data from the 450k. The presentation can be found.