Hi Qing.
I believe what you are referring to is:
p.adjust(..., "BH")

The "fdr" option uses the method of Benjamini, Hochberg, and Yekutieli.
(Not the original Benjamini, Hochberg article)
It might be the method described here:
http://www.math.tau.ac.il/~ybenja/MyPapers/benjamini_yekutieli_ANNSTAT2001.pdf




----------------Contact
Details:-------------------------------------------------------
Contact me: Tal.Galili@gmail.com |  972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
www.r-statistics.com (English)
----------------------------------------------------------------------------------------------




On Sun, Aug 8, 2010 at 11:06 PM, qing chen <qingchen08@gmail.com> wrote:

> Hello,
>
> I am not sure about the p.adjust( , fdr). How do these adjusted p-values
> get?
> I have read papers of BH method. For independent case, we compare the
> ordered p-values with the alfa*i/m, where m is the number of tests. But I
> have checked that result based on the adjusted p-values is different with
> that by using the independent case method.
> Then how do the result of p.adjust( , fdr) come?
> And how can we interpret them?
> Thank you!
>
>
>
> Your truly, Qing Chen
>
>        [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

	[[alternative HTML version deleted]]

