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p.adjust( , fdr)

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p.adjust( , fdr)

qingchen
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

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Re: p.adjust( , fdr)

Tal Galili
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




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On Sun, Aug 8, 2010 at 11:06 PM, qing chen <[hidden email]> 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]]
>
> ______________________________________________
> [hidden email] 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]]

______________________________________________
[hidden email] 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.
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