[BioC] Help on experiment design

[Marcelo Brandão]

Hello all!
I am analyzing a set with 6 microarrays, 3 controls and 3
experimentals. I am interested in look after differentially expressed
genes. My doubt, among a lot of else, is if my experiment is designed
correctly. I am currently using the following comands:

designEsp <- cbind(controle=c(1,1,1,0,0,0),experimento=c(0,0,0,1,1,1))
fitEsp <- lmFit(exprs(summarized),designEsp)
fitEsp <- eBayes(fitEsp)
topTable(fitEsp,coef=2, adjust = "fdr", n = 10)

is it the best way to infer different expression? I am using nimblegen
microarrays.

Thanks in advance.

Marcelo

-- 
Marcelo Mendes Brandão
Postdoc fellow
Laboratório de Biologia Molecular de Plantas - ESALQ/USP
Website: http://bioinfo.esalq.usp.br
AtPIN: http://bioinfo.esalq.usp.br/atpin
SKYPE: mmbrand
Tel: (+55) 19 3429 4442