[R] false discovery rate !

[john seers (IFR)]

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


---
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-----Original Message-----
From: A Ezhil [mailto:ezhil02 at yahoo.com] 
Sent: 10 July 2008 16:23
To: r-help at r-project.org; 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) <john.seers at bbsrc.ac.uk> wrote:

> From: john seers (IFR) <john.seers at bbsrc.ac.uk>
> Subject: RE: [R] false discovery rate !
> To: ezhil02 at yahoo.com, r-help at r-project.org
> 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: r-help-bounces at r-project.org
> [mailto:r-help-bounces at r-project.org]
> On Behalf Of A Ezhil
> Sent: 10 July 2008 15:41
> To: r-help at r-project.org
> 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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