[BioC] How to save result from limma

Jenny Drnevich drnevich at illinois.edu
Wed Oct 22 23:04:53 CEST 2008

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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