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

[kfbargad at ehu.es]

If I am not wrong, section 8.6 of the limma manual explains what you 
want, and that is

fit2$F.p.value

hth,

David 

> 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
> 
> 
> 
> -- 
> 
> **************************************
> Ivan Baxter
> Post-Doc
> Purdue University
> ibaxter at purdue.edu
> 
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