Thanks again for your reply Nianhua. I have found the problem. By looking through the perl scripts I realized that I should not have quotes around my probe ids nor my accession numbers. I edited my file in openOffice's calc which automatically adds those pesky quotation marks. Since read.delim automatically strips of those quotes it wasn't apparent at first. I apologize for wasting your time. I can now successfully create annotation packages using gbNRef. Regards, Cameron