[BioC] Limma Design Matrix: How many levels can each factor have?

[Xia Han]

Hi:

I have a drug treament experiments with 3 factors (cell lines, 
compounds, and time course). There are 3 cell lines, 3 compounds (DMSO 
control, compounds 1 and 2), and 2 time points (4hr and 24hr). When I 
try to build a design matrix by something like this:
design <- model.matrix(~cell.lines*compound*time)
I only get 2 cell lines, 2 compounds (DMSO and compound1) and 2 time 
points.
If I use something like this, which is really what I want to compare:
design <- model.matrix(~cell.lines + compound + compound*time)
I still only get 2 cell lines and 2 compounds in the design matrix.

Anything I did wrong? Please help.

Thanks,

Xia