Correct citation for use of frma with Gene and Exon ST arrays added.
The internal workings of the frma function have been modified to ease the eventual transition AffyBatch (affy) objects to FeatureSet (oligo) objects as input.
Changed the way in which the user can pass their own fRMA vectors to the frma function via the "input.vecs" argument. Previously, the user could supply a partial set of vectors and the remaining ones would be obtained from the default frmavecs packages. In retrospect, this seems very likely to introduce a mistake. Now, the user has to either supply all of their own vectors or use all of the default vectors. If anyone was mixing vectors before, this can still be accomplished by loading the respective frmavecs package and manually creating your own mixture of vectors.
Bug fix: on certain operating systems, due to differences in the locale, the probe ordering returned by the pm function (affy) did not match the order stored in the frmavecs packages. Updated frmavecs packages will now contain the pmindex values for all probes and affy ids for all probesets. Also the frma and barcode functions now check that the order matches. If the order is not the same, these functions attempt to reorder the probes to match.
Added NEWS.Rd file.