[BioC] posterior values in topTable for limma
Adaikalavan Ramasamy
ramasamy at cancer.org.uk
Fri Feb 25 12:41:11 CET 2005
Can I suggest that limma package returns the posterior probabilities
along with the log odds ratio, B ?
I am currently using the following codes to get the posterior values
(unless I am reading the documents wrong).
fit <- lmFit(onebatch, design)
fit2 <- contrasts.fit( fit, contrast.mat )
fit2 <- eBayes(fit2)
results <- topTable(fit2)
results$post.prob <- exp(results$B) / ( 1 + exp(results$B) )
Hopefully this will get people to start thinking in terms of
probabilities and less on p-values.
Thank you.
Regards, Adai
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