Hi Ezhil

Quite possibly.

Look at this simple example based on what you describe:

> p.adjust(c(0.0002, 0.41, 0.4, 0.42,0.43))

[1] 0.001 1.000 1.000 1.000 1.000

Does this fit what you are seeing?

Regards

JS

---

Web sites:

www.ifr.ac.uk

www.foodandhealthnetwork.com

-----Original Message-----

From: A Ezhil [mailto:

[hidden email]]

Sent: 10 July 2008 16:23

To:

[hidden email]; john seers (IFR)

Subject: RE: [R] false discovery rate !

Dear John,

My P values are not same and the smallest P value = 0.0002. My P value

distribution is not that great (see the attached file), most of them are

> 0.4. Do you think this is the reason for getting same FDR vlaues?

Thanks again,

Ezhil

--- On Thu, 7/10/08, john seers (IFR) <

[hidden email]> wrote:

> From: john seers (IFR) <

[hidden email]>

> Subject: RE: [R] false discovery rate !

> To:

[hidden email],

[hidden email]
> Date: Thursday, July 10, 2008, 8:27 PM Hi

>

> Are all your input p values the same? If so your output FDR values

> would be the same.

>

> Or are all your p-values relatively large? Then (nearly) all your FDR

> values might be 1.

>

> Why don't you put a small example up of what you did?

> Then we could see

> what method you used etc.

>

> Regards

>

>

> JS

>

>

>

>

> ---

> -----Original Message-----

> From:

[hidden email]
> [mailto:

[hidden email]]

> On Behalf Of A Ezhil

> Sent: 10 July 2008 15:41

> To:

[hidden email]
> Subject: [R] false discovery rate !

>

> Dear All,

>

> It is not a typical R question (though I use R for this) but I thought

> someone will help me. For the list of P values, I have calculated FDR

> using p.adjust() in R (bioconductor). But my FDR values are same for

> all the P values. When do we get same FDR values? Does the smallest P

> values should less than 1/N? (where N is the number of P values)

>

> Thanks in advance.

>

> Kind regards,

> Ezhil

>

> ______________________________________________

>

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>

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.

______________________________________________

[hidden email] mailing list

https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide

http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.