[BioC] Design/contrast matrix for limma

[Anthony Bosco]

Hi.

How do I set up a design and contrast matrix for the following experiment.

I have unstimulated cells and stimulated cells for individuals with 
and without disease.

sample groups

1	Disease		Unstimulated
2	Disease		Stimulated
3	No Disease	Unstimulated
4	No Disease	Stimulated

Although I can set up design matrix for all two way comparisons, I am 
really interested in what genes are different between disease and no 
disease after stimulation of the cells.

I could take ratios of Unstimulated/stimulated chip data for disease 
and no disease then have only two groups but I am not sure if this is 
optimal.

ie

new sample groups

1	Disease		Stimulated/Unstimulated
2	No Disease	Stimulated/Unstimulated


Any advice gratefully received.


Anthony
-- 
______________________________________________

Anthony Bosco - PhD Student

Institute for Child Health Research
(Company Limited by Guarantee ACN 009 278 755)
Subiaco, Western Australia, 6008

Ph 61 8 9489  , Fax 61 8 9489 7700
email anthonyb at ichr.uwa.edu.au