[BioC] design matrix for timecourse experiment

[Gareth Bloomfield]

Hi,

We are currently planning a timecourse experiment, which will be analysed 
using Limma, and would be grateful for some advice on the design matrix we 
have come up with... Sorry, it's quite complicated and may take some  
figuring out if I haven't explained it as well as I might........

The experiment consists of cells teated with 2 different drugs, with 
samples taken after 3 different times after addition of drug. Instead of 
the simple possibility of comparing everything back to the untreated t0 
sample, we are currently favouring making a loop out of the untreated 
samples (t0, t1, t2, t3), then comparing the two treatments at each 
timepoint to the untreated sample at that timepoint. All comparisons will 
be in both dye orientations.  

The possible design matrix we have is as follows-

Slide	Untreated	        Drug1	          Drug2
     	t1-t0 t2-t1 t3-t2   t1-t0 t2-t1 t3-t2	  t1-t0 t2-t1 t3-t2

1	  1     0     0	      0     0     0	    0     0     0
2        -1     0     0       0     0     0         0     0     0
3	  0     1     0       0     0     0	    0     0     0
4	  0    -1     0	      0     0     0         0     0     0
5	  0     0     1       0     0     0         0     0     0
6	  0     0    -1       0     0     0	    0     0     0
7        -1     0     0	      1     0     0	    0     0     0
8	  1     0     0      -1     0     0	    0     0     0
9        -1     0     0	      0     0     0	    1     0     0
10	  1     0     0	      0     0     0        -1     0     0
11       -1    -1     0	      1     1     0	    0     0     0
12	  1     1     0      -1    -1     0         0     0     0
13       -1    -1     0	      0     0     0         1     1     0
14	  1     1     0	      0     0     0        -1    -1     0
15       -1    -1    -1	      1     1     1	    0     0     0
16	  1     1     1      -1    -1    -1	    0     0     0
17       -1    -1    -1	      0     0     0	    1     1     1
18	  1     1     1	      0     0     0        -1    -1    -1

We hope that this will give us after linear model fitting data 
corresponding to the separate timecourses for the untreated and 2 sets of 
treated cells - have we done this sensibly? 

Many thanks in advance for any advice at all,

Gareth

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