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

[Rory Stark]

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
>
>
>
>	[[alternative HTML version deleted]]
>


NOTICE AND DISCLAIMER
This e-mail (including any attachments) is intended for ...{{dropped:16}}