[BioC] Limma question

[alex lam (RI)]

Dear colleagues,
Hi, I would like to ask a question related to creating design matrix in
limma. Statistics is not my strong subject so I apologise in advance if
this is a silly question. I have a number of arrays with 3 different
treatments and I can generate a design matrix using modelMatrix.

> modelMatrix(targets, ref="Pool")
Found unique target names:
 one Pool three two 
       one three two
samp01   1     0   0
samp02   0     0   1
samp03   1     0   0
...etc

But there are other nuisance factors, for example the arrays were
hybridised in 3 different labs, and the animals are not all from the
same line. I am only interested in comparing the treatment effect but in
the analysis I would like to account for the nuisance factors. I have
been reading the limma user guide and I guess this is a not really
factorial design, correct? Any idea on how to make this matrix?

Regards,
Alex

------------------------------------
Alex Lam
PhD student
Department of Genetics and Genomics
Roslin Institute (Edinburgh)
Roslin
Midlothian EH25 9PS

Phone +44 131 5274471
Web   http://www.roslin.ac.uk