Table 1 R/Bioconductor packages for the processing and analysis of array-based DNA methylation data

Quality control samples

IMA, HumMethQCReport, methylkit, MethyLumi, preprocessing and analysis pipeline, minfi

Quality control probes

IMA, HumMethQCReport, lumi, LumiWCluster, preprocessing and analysis pipeline, wateRmelon

Background correction

Limma, lumi, MethyLumi, minfi, preprocessing and analysis pipeline

Normalisation

Combat^a, HumMethQCReport, lumi, minfi, TurboNorm, MethyLumi, wateRmelon

Type 1 and 2 probe scaling

IMA, minfi, wateRmelon

Batch/plate/chip/confounder adjustment

Combat^a, CpGassoc, ISVA, MethLAB

Data dimension reduction

MethyLumi

Differential methylation analysis/region-based analysis

CpGAssoc, IMA, limma, methylkit, MethLAB, MethVisual, minfi, EVORA

Clustering/profile analysis

Lumi, ISVA, HumMeth27QCReport, methylkit, RPMM, SS-RPMM^b

Multiple testing correction

CpGAssoc, methylkit, MethLAB, NHMMfdr