Changes in version 1.15.2 o Updated gsameth to take into account that some CpGs map to multiple genes. For a small number of gene families, this previously caused their associated GO categories/gene sets to be erroneously overrepresented and thus highly significant. o Updated gometh to call gsameth to perform statistical testing for GO categories and KEGG pathways; goana and kegga are no longer used. o Replaced use of the AnnotationDbi 'toTable' function with 'select' to speed up execution. o The 'topGSA' function is now used to look at the top ranked results from both gometh and gsameth. The vignette has been modified accordingly. o Updated getMappedEntrezIDs, gometh and gsameth to to speed up execution by taking the array annotation in as an optional argument. o missMethyl now uses the latest IlluminaHumanMethylationEPICanno.ilm10b2.hg19 annotation by default for EPIC arrays. Changes in version 1.15.1 o Added getAdjusted function for extracting RUVm adjusted data for visualisation purposes o Updated vignette to demonstrate use of getAdjusted function o Vignette now includes an example of how to handle cases with RUVm where number of samples is greater than number of Illumina negative controls Changes in version 1.7.3 o modified gene set testing functions gometh and gsameth to accommodate EPIC arrays Changes in version 1.5.1 o New gene set testing function gsameth() added, kegg testing functionality added to gometh(). Changes in version 1.1.10 o This version of the package contains functions to perform SWAN normalisation, RUV normalisation and differential methylation analysis, differential variability analysis and gene ontology testing for the 450K array. Changes in version 1.1.3 o Added the gometh function to perform gene ontology analysis. Changes in version 1.1.2 o Added functions to perform RUV normalization and differential methylation analysis. Changes in version 0.99.9 o This version of the package has all calculations in matrix formulation and handles nuisance parameters appropriately. Changes in version 0.99.7 o Added new function, contrasts.varFit. Changes in version 0.99.6 o Modified getLeveneResiduals Changes in version 0.99.5 o Modified the varFit function to accept DGEList objects for differential variability testing for RNA-Seq data. Changes in version 0.99.4 o First version of package contains functions to perform SWAN normalisation and differential variability analysis for DNA methylation data from Illumina's Infinium HumanMethylation450 beadchip.