[BioC] FDR default in edgeR

James W. MacDonald jmacdon at uw.edu
Wed Sep 3 16:56:17 CEST 2014

Hi Son,

If I understand your question correctly, there is no default. In other
words, if you look at the api for topTags, you see:

topTags(object, n=10, adjust.method="BH", sort.by="PValue")

and there isn't anything there to threshold the results by FDR. However,
you can use decideTestsDGE:

decideTestsDGE(object, adjust.method="BH", p.value=0.05)

which will allow you to select an FDR (or other (un)adjusted p-value) on
which to threshold, or you can use the default of 0.05.



On Wed, Sep 3, 2014 at 12:46 AM, Son Pham <spham at salk.edu> wrote:

> Hi All,
> Could you let me know what is the default value (or recommended value) for
> thresholding the FDR in edgeR?
> Thanks,
> Son.
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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