[BioC] limma: get all sig genes from multiple contrasts

Ivan Baxter ibaxter at purdue.edu
Fri Jun 9 08:35:25 CEST 2006

I realize this may be a silly question, but I have gone through all the 
case studies in the limma users manual and I can't seem to find the 
answer to this anywhere.   I have a 3x3 factorial experiment and I 
followed the case studies to make my linear model and designate 13 
contrasts of interest.  My question is: is there a simple way to get all 
the genes that show significant differences in any one of my contrasts? 
(for use in clustering, for ex.)
I manged to pull them out using:

results <- decideTests(fit2)
abres <- abs(results)
sig_gene <- abres[rowSums(abres) > 0,]

which then has to be linked up by

test <- match(rownames(sig_gene), geneNames(eset))
sigchange <-  eset[test]

This seems rather ungainly when compared to how elegantly all the other 
functions in limma work. Is there a simpler way to do this?



Ivan Baxter
Purdue University
ibaxter at purdue.edu

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