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

[NEIL-BERNET Helen]

Rory,

Thanks for your answer.
I've already tried DiffBind, it gave me roughly the same results as edgeR,
hopefully!
Indeed, it's easier for ChIP-seq, but I couldn't address 2 things:

1) I need to use quantile normalization (with limma package) prior to
differential analysis, I'm not sure that's possible to use directly my own
normalized counts. Moreover, I don't use peak calling, because I study
specific regions, for example promoter proximal regions, so I don't have
any affinity score.

2) I couldn't find a way to analyze my data without replicates, and that's
a critical point for ChIP-seq, most of the times, we don't have any
replicates!
If you can answer these questions, I would really appreciate to work with
DiffBind instead of edgeR!!

Thank you very much,

helen



Le 25/01/12 16:33, << Rory Stark >> <Rory.Stark at cancer.org.uk> a écrit :

>Hi helen-
>
>After calling exactTest, you can call topTags with the result. topTags
>takes a parameter, n, which is the number of results to return -- if you
>set it to the total number of sites you are comparing, you will get them
>all back with their associated stats. I end up doing something like:
>
>> results = topTags(de$db,nrow(db$counts))$table
>
>
>to get everything back.
>
>If you are using edgeR to do differential binding analysis of ChIP-seq
>data, you may also want to check out the DiffBind package, which add
>functions to make this sort of thing easier.
>
>Cheers-
>Rory
>
>On 25/01/2012 15:14, "NEIL-BERNET Helen" <helen.neil-bernet at cea.fr> wrote:
>
>>Dear all,
>>
>>I use edgeR for differential analysis of ChIP-seq densities.
>>I would like to know how to export the results from 'exactTest',
>>including p-values and FDR.
>>Using 'topTags', I only have the 10 first results, with p-values and FDR.
>>But when I do 'write.table(mytest$table, Š)', it gives me only the
>>complete set of p-values, but not the FDR.
>>
>>Thanks for your help,
>>
>>Best regards,
>>
>>helen
>>
>>
>>
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>>
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