[BioC] How to save result from limma

Jenny Drnevich drnevich at illinois.edu
Tue Oct 28 15:17:09 CET 2008

Everything seems to work fine now. The sort="none" option will really 
come in handy - Thanks!!


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
>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!
>>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
>>>>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!
>>>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
>>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
>>ph: 217-244-7355
>>fax: 217-265-5066
>>e-mail: drnevich at illinois.edu

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