Hi, I've implemented GCRMA as an option in affylmGUI 1.0.4. Obviously you need the gcrma package installed to use it. Currently you can only use the default options for gcrma, but if gcrma users let me know which options are most useful, I'd be happy to put their implementation high on my priority list of things to do in affylmGUI. I've also implemented (in affylmGUI 1.0.4 and limmaGUI 1.0.3) a dialog allowing the user to enter a P-Value cutoff for Venn Diagrams. It accepts R expressions (e.g. 0.05 or 1/20) Also, loading either package whilst the other is already loaded now gives an error saying "Please run limmaGUI and affylmGUI in separate R sessions". New versions can be installed with: install.packages("affylmGUI", contriburl="http://bioinf.wehi.edu.au/affylmGUI") install.packages("limmaGUI", contriburl="http://bioinf.wehi.edu.au/limmaGUI") Jeff, can you please put these on BioC-devel at some stage. As usual, they are at: http://bioinf.wehi.edu.au/affylmGUI/ [ or as a direct link ] http://bioinf.wehi.edu.au/affylmGUI/affylmGUI_1.0.4.tar.gz AND http://bioinf.wehi.edu.au/limmaGUI/ [ or as a direct link ] http://bioinf.wehi.edu.au/limmaGUI/limmaGUI_1.0.3.tar.gz Thanks, James