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.