Update affylmGUI to use AnnotationDbi and the new ".db" style probe-set annotation packages.
Reduce overlap with the limma package. affylmGUI now uses the limma functions lmFit(), eBayes(), topTable() and limmaUsersGuide() directly.
Remove functions ALGchangeLog(), ALGlimmaUsersGuide(), deleteItemFromList(), toptable2() and topTable2().
Add affylmGUI-package help file. Split existing help file into two.
Various internal code updates and simplifications.