missMethyl-package

missMethyl

missMethyl is a library for the analysis of Illumina's 450K human methylation BeadChip. Specifically, functions for SWAN normalisation and differential variability analysis are provided. SWAN normalisation uses probe specific information, and the differential variability procedure uses linear models which can handle any designed experiment.

Normalisation and testing for differential variability and
	differential methylation for data from Illumina's Infinium 
	HumanMethylation450 array. The normalisation procedure is 
	subset-quantile within-array normalisation (SWAN), which allows 
	Infinium I and II type probes on a single array to be normalised 
	together. The test for differential variability is based on an 
	empirical Bayes version of Levene's test. Differential
	methylation testing is performed using RUV, which can adjust for
	systematic errors of unknown origin in high-dimensional data by
 	using negative control probes. Gene ontology analysis is performed
 	by taking into account the number of probes per gene on the
 	array.

missMethyl-package: Introduction to the missMethyl package

Description

Arguments

Details

References