[BioC] fdr adjustment in limma

[Gordon K Smyth]

> How does the method "fdr" in limma work? Strictly speaking, I am not
> aware that fdr methods actually adjust p values but rather set p value
> cut-offs according the a value q, the user defined acceptable proportion
> of false positives.

Any decision method including fdr can be expressed in terms of adjusted
p-values.  Please type ?p.adjust and follow the last cited reference.

> The set of all tests with a p value less than or
> equal to the cut-off would be expected to have a false positive rate of
> the value q.
>
> I have played around with limma's fdr method a bit and I get the feeling
> that, after fdr correction using p.adjust, perhaps I should set my own p
> value tolerance equal to my FDR tolerance. In other words, if I am
> willing to accept an FDR of 10%, after applying p.adjust, I should
> accept all tests with p<0.10 as significant.

Yes, that's right.  That is the way that all p-value adjustment methods work.

Gordon

> Am I right or wrong on this?
>
> Thanks,
>
> Mark
> Mark W. Kimpel MD