[BioC] limma example Weaver Data

[Gordon Smyth]

The easiest way to handle these sort of direct designs (e.g., loop designs) 
in general is to choose one of the RNA sources to play the role of a 
reference source for the purposes of the design matrix.

Have you read the section on "Direct Two-Color Designs" in the limma User's 
Guide? In limma 1.9.6, this is Section 9.4 of the guide. The design matrix 
given on page 22 could also have been created using

design <- modelMatrix(targets, ref="CD4")

Gordon

At 01:32 AM 1/06/2005, Wenbin Liu wrote:
>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