[BioC] How to save result from limma

[Gordon K Smyth]

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 
>