Version 1.10.2 of affylmGUI has been submitted to the Release version of Bioconducor. Unfortunately some bugs slipped past me in version 1.10.0 of affylmGUI. The main ones related to not using accessor functions for certain objects. Also the ExpressionSet objects returned by rma and gcrma and the PLMset object returned by fitPLM were not handled correctly by affylmGUI. It now correctly extracts the expression and se.expression values into matrices. Also the heatdiagram will now save as a PNG/JPG/PDF. It seems it never did!. As version 1.10.0 always gave an error message on the initial reading of datafiles, I suggest all users upgrade to the new version asap, Keith Satterley Maintainer of affylmGUI. PS. ver 1.10.2 will be submitted to the devel branch in the next 24 hours. I away from my office at the moment.