[BioC] nested design with random factor and limma???

[Bettina Kulle Andreassen]

hi,

i have the following dataset:
- 26 indivuals with expressiondata (log-ratio from common ref design)
(random factor: patient)
- each individual has expression data from 1 to 3 different (but fixed)
locations (fixed factor: location)
- 14 controls, 12 patients (fixed factor: group)

i am mainly interested in the group effect!

i tried limma, but it did not seem to work with my random
factor patient?.

any suggestions?
thanks for help!

tina

-- 

Bettina Kulle Andreassen
Associate Professor

University of Oslo
Faculty Division Ahus
Institute for clinical epidemiology 
and molecular biology (Epi-Gen)

Sykehusveien 27
N-1474 Nordbyhagen

tel: +47 67927762
fax: +47 67927803