[R] Benjamini-Hochberg (BH) Q value (false discovery rate)

[David Bars]

Dear everybody,

I'm using stats package (version 3.5.2) and in detail their p.adjust()
function in order to control the false discovery rate in multiple
comparisons. In particular I used the Benjamini-Hochberg method.

Nevertheless,  the help of the stats package indicates that the adjusting
method is based on:
Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery
rate: a practical and powerful approach to multiple testing. Journal of the
Royal Statistical Society Series B, 57, 289–300.
http://www.jstor.org/stable/2346101.

But, in the function mentioned above (p.adjust()) there are no possibiity
to define the Q value (the false discovery rate). I understand that the Q
value is calculated automatically but through which method???

For example, in another package (sgof v.2.3 also deposited on CRAN)
indicates that the the false discovery rate is estimated by the method
developed by:

Dalmasso C, Broet P and Moreau T (2005). A simple procedure for estimating
the false discovery rate. *Bioinformatics* 21:660--668.


Many thanks for your help,

David Bars.

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