Changes in version 1.1: o Changed NAMESPACE file o Defined constructors for MethylSet, RGChannelSet, RGChannelSetExtended. o Included a version number in the class definition for MethylSet and RGChannelSet. Old objects can be updated by calls of the form updateObject(Mset). o read.manifest (not exported) updated to include nCpGs. o preprocessSwan was added. Still work in progress. o Changed background calculation in preprocessSwan. o Added a section to the vignette describing preprocessSwan. o Bug fix: ilogit2 is now in base (it used to be base e). Thanks to Time Triche, Jr . o Added and dcoumented the IlluminaMethylationAnnotation class; still work in progess. o Moved package vignette from inst/doc to vignettes. Changes in version 0.99: o Initial release to Bioconductor. o Added NEWS file. o Bugfix to vignette. o readIDAT is now exported by crlmm, implying that we can import this function through NAMESPACE.