[BioC] factorial experiment matrix design

[Mikko Arvas]

Hi,

reading the BioC list I see that things like this are asked often, but I am 
sorry I just can't get this. Could somebody show me how to do it:

I have a microarray experiment with 2 strains and 3 time points from each, 
so I would like to do 2x3 factorial experiment
to get all the genes that change in strain A (or B) during time series (10, 
30, 60 min) and between strains in all the time points.

So trying to follow limma guide, the design matrix object would be 
something like this (with 2 repeats for each):

 > dQex
    (Intercept) Qexa10 Qexa30 Qexa60 Qexb10 Qexb30
1            1      1      0      0      0      0
2            1      1      0      0      0      0
3            1      0      1      0      0      0
4            1      0      1      0      0      0
5            1      0      0      1      0      0
6            1      0      0      1      0      0
7            1      0      0      0      1      0
8            1      0      0      0      1      0
9            1      0      0      0      0      1
10           1      0      0      0      0      1
11           1      0      0      0      0      0
12           1      0      0      0      0      0
attr(,"assign")
[1] 0 1 1 1 1 1
attr(,"contrasts")
attr(,"contrasts")$Qex
     a10 a30 a60 b10 b30
a10   1   0   0   0   0
a30   0   1   0   0   0
a60   0   0   1   0   0
b10   0   0   0   1   0
b30   0   0   0   0   1
b60   0   0   0   0   0

What kind of contrast (or as well design) matrix do I need to get all the 
changing genes out?

Cheers,
Mikko



Mikko Arvas
VTT Biotechnology

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