[BioC] permutation test

[James W. MacDonald]

Hi Patricia,

I think John was getting at the fact that 'randomization test' has no 
specific meaning in statistics, other than the obvious fact that you 
want to permute things. If you state clearly what you are trying to do 
you will have a much better chance of getting an answer, not to mention 
probably getting the correct answer.

Best,

Jim



Patricia wrote:
> 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]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623