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

[NEIL-BERNET Helen]

Mark,

topTags(de, n=Inf) is perfect! I could obtain the full table.


Thanks a lot!
helen


Le 25/01/12 16:28, « Mark Robinson » <mark.robinson at imls.uzh.ch> a écrit :

>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, Š)', 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
>University of Zurich
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>
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