VERSION	NEWS
1.3.1	Changed annotation method for tost() (minfi and methylumi methods.
	thanks to several users for bug reports!
0.99.16	replaced dependency on ROCR with ROC (bioconductor) package
	seabird() no longer takes a vector for the stop argument

0.99.15	codoc corrections.  
	temporarily removed dependency on ROCR (and thus gdata)

0.99.14	MethylSet methods [dn]a[st]e[nt] now return objects containing 
	normalized intensities as well as betas
	fixed a bug in as.methylumi

0.99.13	fixed swan wrapper generic and MethyLumiSet method bugs 

0.99.12	methods d**** now have ... argument so that data without
	Sentrix IDs should work (thanks to Elodie Portales-Casamar
	for bug report).

0.99.11	RGChannelSetExtended pfilter method bug fixed

0.99.10	BioConductor submission

0.9.8	MethyLumiSet methods now update history slot

	new MethyLumiSet method for pfilter

	RGtoy2 removed from data(minfitoy).  This is because minfi 
	now expects the manifest to be a package.

	swan function patched so that it can process subsets of array data
	(provided by Jovana Maksimovic).  Now works with melon data set.

	as.methylumi generic function added. Gets fData from 
	package:IlluminaHumanMethylation450k.db . The MethyLumiSet method 
	is useful for ensuring methylumi objects contain this data.

	Andrew Teschendorff's BMIQ function and a MethyLumiSet method
	added 
	
	minfi 1.4.0 has a changed manifest structure resulting in
	SNP probes being left out of the MethylSet.  This breaks genki()
	for the minfi objects and also the minfitoy data() set. 



