Hello all,

 

Gordon Smith helpen me a while ago with calculating regularised p-values
(paired t-test) using Limma. This is the R-code he gave to me:

 

Y <- as.matrix(<gcrma normalized values>)

 

Sample <- factor(rep(1:4,each=2))

BeforeAfter <- factor(rep(1:2,length=8))

design <- model.matrix(~Sample+BeforeAfter)

 

fit <- lmFit(Y,design)

fit <- eBayes(fit)

topTable(fit, coef="BeforeAfter2", adjust="fdr")

 

Now I want to investigate the effect of the regularisation, so I also
want to calculate the ordinary p-values. One would say that this can be
easily done by leaving the following line out:

 

fit <- eBayes(fit)

 

Unfortunately, topTable expects a model that has been eBayes()
corrected. So, I am lost. How can I calculate the ordinary paired
p-values using Limma?

 

Regards,

 

Philip


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