VERSION	NEWS

1.03	paper is out in BMC Genomics.  CITATION file added.

1.0.2	fixed bug in danes generic, now works with methylumi objects again. Thanks to Joana Viana for bug report.

1.0.1	corrected error in combo.R (thanks to Marco Boks for bug report)

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.  

