[BioC] limma example Weaver Data

[Wenbin Liu]

Thanks, Gordon! In the expanded example, you have a
common RNA source, the Pool. What if one doesn't have
a common RNA source, such as when it is a loop design
with more than three arrays like the unexpanded Weaver
data? Can you please show me how to generate the
matrices? Thanks!


Wenbin

--- Gordon K Smyth <smyth at wehi.EDU.AU> wrote:

> I guess that you are using an older version of the
> software.  The Weaver example was expanded and
> simplified last October, and full commands are now
> given to compute the design matrix, including
> use of modelMatrix() and makeContrasts().
> 
> Gordon
> 
> ------ original message --------
> [BioC] limma example Weaver Data
> Wenbin Liu wnbnl at yahoo.com
> Thu May 26 23:25:09 CEST 2005
> 
> Dear Gordon and limma users,
> 
> I'm struggling to understand the design matrices in
> the Weaver Data in the Case Studies section of the
> limma User's Guide.
> 
> In the single loop design, there are 4 arrays and 4
> conditions (from two time points and two genotypes).
> I tried using modelMatrix() with the target from the
> example and assigning ref='P11WT'. I would like to
> check the effect 'TimeWt' which is the late vs.
> early
> for WT. Unfortunately, I have been unable to get
> Gordon's result (topTable result).
> 
> Can someone show me how to get Gordon's design
> matrices (two of them in that example) by using the
> function modelMatrix() and probably plus
> makeContrasts()?
> 
> Thanks in advance!
> 
> Sincerely,
> Wenbin
> 
> 
> 
>