[BioC] permutation test

[M Perez]

Hi Patricia,

I assume you need a randomization test for calculating
the FDR or the FWER for multitesting, thus the number
of usefull permutaions is limited by the number of
your samples. 

I would recomend you to check the siggenes
packages,where you can setting the number of
permutations.  

Best 
Manuel 
--- Patricia <patricia.garcia at integromics.com>
escribió:

> Hi,
> My question is about the number of permutations in a
> randomization test. I
> would need to make a very large number of
> permutations (around 10000) and I
> can't find a function that calculates the pvalue
> from that.
> 
> 
> Thanks
> 
> Patricia
> 
> -----Original Message-----
> From: john seers (IFR)
> [mailto:john.seers at bbsrc.ac.uk] 
> Sent: miércoles, 12 de marzo de 2008 12:04
> To: Patricia; bioconductor at stat.math.ethz.ch
> Subject: RE: [BioC] permutation test
> 
>  
> 
> 
> Hi
> 
> I don't really understand your question but perhaps
> these functions may
> help:
> 
> ?sample
> ?combn
> 
> Regards
> 
> John Seers
> 
> 
>  
> ---
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On
> Behalf Of Patricia
> Sent: 12 March 2008 10:46
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] permutation test
> 
> Hi everyone,
> 
>  
> 
> Is there any function to apply a randomization test
> (permutation test)
> in witch you can choose the number of permutations?
> 
> I've using function perm.test but I need to make
> more permutations.
> 
>  
> 
> Thanks!
> 
>  
> 
> Regards
> 
>  
> 
> Patricia
> 
>  
> 
>  
> 
>  
> 
> 
> 	[[alternative HTML version deleted]]
> 
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