Hi, Some of you might have come across the reference: Li Zhang, Michael F. Miles and Kenneth D. Aldape - A model of molecular interactions on short oligonucleotide arrays, 2003, Nature Biotech., vol. 21, n.7 There is now a R package doing it. It extends the Bioconductor package affy. Because of time constraints on my side, it was developped under R-1.7.1. I will move to Bioconductor as soon as it is checked against R-1.8.0 (it *seems* to work under 1.8.0, but you are welcome to report odd things you would notice). We made some recent changes in our code to try to speed it up (because it was slooooow, and still is), which hopefully did not introduce bugs in the computations. We would be happy to hear about such things if one observes them. The extension package works with the current release of 'affy' (version 1.2.x) and should work with the devel version too. The source for the package is available in the CVS section of Bioconductor. A compiled version for Windows and the source tarball are available at: http://www.cbs.dtu.dk/laurent/download/affypdnn/ Laurent