Dear all, In GeneAnswers, when I run this getGOList(c('56458', '16590'), 'org.Mm.eg.db', GOCat='BP', level=2) switch level=2 to level=3 for GOCat='BP' it is working (indicating different GO number) but when I set up GOCat='CC' between level=2 and level=3 has the same GO number why the level has not effect on GO number when I set up GOCat='CC' length(getGOList(c('56458', '16590'), 'org.Mm.eg.db', GOCat='BP', level=2)) [1] 314 > length(getGOList(c('56458', '16590'), 'org.Mm.eg.db', GOCat='BP', level=3)) [1] 246 > length(getGOList(c('56458', '16590'), 'org.Mm.eg.db', GOCat='CC', level=3)) [1] 43 > length(getGOList(c('56458', '16590'), 'org.Mm.eg.db', GOCat='CC', level=2)) [1] 43 thanks Zhi Zhang, Ph. D. Sanford-Burnham Medical Research Institute Building 7, Bodmer lab 10901 North Torrey Pines Rd. La Jolla, CA 92037, USA Phone 858-646-3100 ext. 3801 Fax 858-795-5298 [[alternative HTML version deleted]]