Hi, I've just uploaded limmaGUI_1.1.2 to : http://bioinf.wehi.edu.au/limmaGUI/ It has some bug fixes: - When the user chose not to use background correction, limmaGUI gave an error "BCMethod undefined". Fixed now. - In the color-coded MA plots, the title was being set twice, once by the main= argument and once by title(). This is fixed now. The main argument of plotMA is now set to "" and then title() is used. This is because limmaGUI uses tkrplot which gives warnings when using main=. - Exporting an HTML report failed if used immediately after loading in a data set, because the array layout wasn't yet defined. This is fixed now. The array layout is now defined immediately after reading in the GAL file. - The function plotMAlimmaGUI has been removed from plot.R. This was just a temporary function used while experimenting with new arguments added to limma's plotMA function. But now that limma has these new arguments, plotMAlimmaGUI is no longer needed. All calls to plotMAlimmaGUI (including one in the HTML report function), have now been replaced with calls to plotMA. Regards, James