Normalisation
Normalisation involves making changes to the raw data in order to remove artifactual variation. In the case of Illumina 450K BeadChip arrays, this requires correcting for the presence of two different probe types. Infinium I probes use the same colour signal for methylated and unmethylated CpG and are often used for regions of high CpG density, while Infinium II probes use different colours to differentiate between methylated and unmethylated states (Numerous methods exist for normalising Illumina BeadChip array data, but there is little consensus or guidance on which should be employed in a given context. The main advice is that between-array methods, which normalise across samples, are preferable when global differences between samples are expected, while within-array methods, which normalise probes within each sample, are better suited to effects in which the majority of genes will not be differentially expressed. (Both Subset Quantile Normalisation and Subset-Within-Array-Normalisation were performed using functions in the 