[BioC] edgeR package : question about 'exactTest' results

[Mark Robinson]

Hi Helen,

You can do this manually.  Using the example from the exactTest() docs:

-----
     # generate raw counts from NB, create list object
     y <- matrix(rnbinom(80,size=1/0.2,mu=10),nrow=20,ncol=4)
     rownames(y) <- paste("Gene",1:nrow(y),sep=".")
     group <- factor(c(1,1,2,2))
     d <- DGEList(counts=y,group=group,lib.size=rep(1000,4))
     
     # estimate dispersions and find differences in expression
     d <- estimateCommonDisp(d)
     d <- estimateTagwiseDisp(d)
     de <- exactTest(d)
-----

Then, something like:

outtab <- cbind(de$table, FDR=p.adjust(de$table$p.value,method="BH"))
write.table(outtab, "my.txt" )

or:

tt <- topTags(de, n=Inf)
write.table(tt, "my.txt" )

The latter is sorted, the former isn't.  Hope that helps.

Regards,
Mark


On 25.01.2012, at 16:14, NEIL-BERNET Helen wrote:

> Dear all,
> 
> I use edgeR for differential analysis of ChIP-seq densities.
> I would like to know how to export the results from 'exactTest', including p-values and FDR.
> Using 'topTags', I only have the 10 first results, with p-values and FDR.
> But when I do 'write.table(mytest$table, …)', it gives me only the complete set of p-values, but not the FDR.
> 
> Thanks for your help,
> 
> Best regards,
> 
> helen
> 
> 
> 
> 	[[alternative HTML version deleted]]
> 
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Prof. Dr. Mark Robinson
Bioinformatics
Institute of Molecular Life Sciences
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