[BioC] Paired samples and origin question, Limma

[Morten Mattingsdal]

Hello everyone,

First: Im really sorry for posting this because Ive found several topics 
in the mail archive, but I cant seem to get any smarter.

Backgound: I have 6 patients which cells have been divided into two 
groups: annexin positive and annexin negative, thus having 12 samples 
from 6 patients. In addition the 12 Affymetrix arrays have been produced 
at two differet labs. I want to correct for the variance introduced by 
the different labs and biological differences from the repsective 
patients. As I understand it I can use the block option in lmFit to 
correct for this.

Do the following Limma code correct for the origin of the samples, and 
how can I add information that the samples are paired by patients ?
Should I use an ANOVA model for this instead of a Limma linear model ?

design <- model.matrix(~ -1+factor(c(1,1,1,1,1,1,2,2,2,2,2,2)))
colnames(design)=c("positive","negative")
origin=c(1,1,1,2,2,2,1,1,1,2,2,2)
dupcor <- duplicateCorrelation(eset,design,block=origin)
fit <- lmFit(eset,design,block=origin,correlation=dupcor$consensus)
contrast.matrix <- makeContrasts(positive-negative, levels=design)
fit2 <- contrasts.fit(fit, contrast.matrix)
fit2 <- eBayes(fit2)

To sum up, I want to ask limma this: "Give me DE genes from Annexin 
positive vs Annexin negative after taking into account that the samples 
are paired patient and location wise"

be gentle with me. Im only a biologist :)
morten