Changes in version 1.3:

    o   Updated preprocessSwan to fix a bug when mSet was not set to the
	default value of NULL.  Specifically, now the "counts" tables is
	used to construct "subset".

    o   Changed the function manifestNew() to
	IlluminaMethylationManifest().

    o   Added IlluminaMethylationAnnotation().

    o   Added placeholders for unit testing based on RUnit.

    o   Introduced a new show method for MethylSet and RGChannelSet,
	derived from the eSet method in Biobase.

    o   The annotation slot of a MethylSet/RGChannelSet is now intended to
	_not_ be a scalar, but instead have length 2 with components
	'array' and 'annotation'.  This foreshadows introdution of
	annotation packages for use with minfi.

    o   Reorganization of R files; rewriting of the man pages for
	MethylSet, RGChannelSet.

    o   getMeth, getUnmeth, getBeta, getM are now methods.

    o   bug fix to qcReport thanks to Tao Shi.

    o   Changes to getBeta / getM, both in terms of which arguments the
	methods take and how the values are computed.

    o   Changes to the manifest structure; it now has separate slots for
	genotype probes and these probes are no longer part of a MethylSet
	(using eg. preprocessRaw).  They can be accessed using
	getProbeInfo(rgSet, type) with type equal to "SnpI" or "SnpII".

    o   Introduction of mapToGenome, getLocations and the new class
	GenomicMethylSet.  man pages are reasonably complete, still need to
	add examples to the vignette.  This will be a standard part of an
	extended pipeline.

    o   Introduction of IlluminaHumanMethylation450lannotation.ilmn.v1.2
	which contains some new annotation needed for
	mapToGenome/getLocations.  This package will be split into several
	packages moving forward, in an attempt to harmonize efforts by us
	and Tim Triche.  getLocations/mapToGenome will stay the same.

    o   getControlTypes added (returns the different types of control
	probes).

    o   GenomicMethylSet now inherits a number of methods including
	granges(), start(), end() etc. from SummarizedExperiemnt.  They
	have therefore been deleted from minfi.

    o   Bugfix to getLocations(..., mergeManifest = TRUE).  It now longer
	throws an error.

    o   mapToGenome now returns a GenomicMethylSet ordered according to the
	chromosome name ordering chr1,..,chr22,chrX,chrY,unmapped, the last
	one not present if drop=TRUE (default).

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 <tim.triche@gmail.com>.

    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.