[BioC] limma factorial designs in two color arrays

[Sean Davis]

On 1/10/06 2:19 AM, "Yong Jiang" <yjiang at ucsd.edu> wrote:

> hi,
> i am using limma to analyze agilent chip data with four groups of cell
> lines: wt, mut, wt+S(stimulated), mut+S.
> goals: 1)find genes difference between wt and mut; 2)which genes
> response to S in wt and mut repectively; 3) which genes respond
> differently in mut and wt.
> 
> can anyone tell me how to design a matrix model for the comparison ?
> thanks.

This is a 2x2 factorial design.  There are good examples in the limma user
guide.  The weaver mutant data are from a two-color 2x2 factorial design.
That section should be particularly helpful.

Sean