gordon, for the last release of affy (1.2.x) i followed, as best i could, your recommendations for documenting the normalize method. with the latest R im getting the following warning * checking Rd \usage sections ... WARNING Objects in \usage without \alias in documentation object 'normalize-methods': normalize if i put an alias for normalize in this documentation object, as suggested by R check, then the help for normalize will once again become affy specific. the problem is that the "usage" for normalization in affy is "normalize(object,...)" but if i put that in the help file for the affy specific normalization documentation i get the above warning. for now, im simply removing "normalize(object,...)" from the usage section since it is described in the details section. this seems to have gotten rid of the warning and i dont think the help file lost much. but, if you have any suggestions please let me know. -r