[BioC] limma factorial designs in two color arrays

[Yong Jiang]

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.

yong