Dear Ying, Laurent and others who have had difficulties with exporting data from expression sets. To export data, use the following command on the normalised data ( with the marrayInput library open ). This should work on both versions of R. write.table( maM(name.norm) , file="Normalized Results.xls" , sep="\t" , row.names=maLabels(maGnames(name.norm))) An updated and expanded version of the "Biologists Guide" will be completed in the coming weeks that will correct for such changes. I will send notice out when it is finished for those that are interested. Alternatively the limma package (and GUI ) is very good and is fairly simple to understand. Regards Chris Bye [[alternative HTML version deleted]]