Everything seems to work fine now. The sort="none" option will really come in handy - Thanks!! Jenny At 10:07 PM 10/22/2008, Gordon K Smyth wrote: >Dear Jenny, > >Thanks for the heads-up. I believe I have fixed it entirely now in >limma 2.16.2. Try it out and see if you can break it. > >Best wishes >Gordon > >On Wed, 22 Oct 2008, Jenny Drnevich wrote: > >>Hi Gordon, >> >>I just downloaded the new R 2.8.0 release and limma 2.16.0. I was >>checking out the new sort="none" option in topTable and I found an >>error in the help page for ?topTable. It doesn't list >>sort.by="none" as a possibility for topTable or toptable, but does >>list it for topTableF. However, it's actually the reverse; >>sort.by="none" works when using topTable with only 1 coef but not >>with more than 1 coef. Just thought I'd let you and the archives know... >> >>Thanks again! >>Jenny >> >>At 07:15 PM 8/19/2008, Gordon K Smyth wrote: >> >> >>>On Tue, 19 Aug 2008, Jenny Drnevich wrote: >>> >>>>At 06:14 PM 8/13/2008, Gordon K Smyth wrote: >>>>>OK, I've added sort="none" to the possibilities. >>>>>Best wishes >>>>>Gordon >>>>Hi Gordon, >>>>Should this change to topTable be up on BioC by now? I just >>>>updated my packages on R 2.7.1 and the latest limma_2.14.5 does >>>>not have it. Neither does the developmental version limma_2.15.10 >>>>on R 2.8.0 dev. Usually your changes appear very quickly... >>>>Thanks again for adding it! >>>>Jenny >>>Not committed to BioC yet. I'm getting older and slower. Also, >>>there will be a number of code additions in my next commit to >>>BioC, which I'm still finalising. >>>Best wishes >>>Gordon >> >>Jenny Drnevich, Ph.D. >> >>Functional Genomics Bioinformatics Specialist >>W.M. Keck Center for Comparative and Functional Genomics >>Roy J. Carver Biotechnology Center >>University of Illinois, Urbana-Champaign >> >>330 ERML >>1201 W. Gregory Dr. >>Urbana, IL 61801 >>USA >> >>ph: 217-244-7355 >>fax: 217-265-5066 >>e-mail: drnevich at illinois.edu