[BioC] SAM siggenes number of permutations

[Holger Schwender]

Hi Claus,

this is not totally correct. If none of the permuted test scores is larger than the actual test score, then your p-value will be 0.

Moreover, SAM uses not just the B permuted test scores of a particular gene to compute its p-values, but all mB permuted test scores of all m genes such that the p-value of a gene is given by i/mB instead of i/B, where i is the number of more extreme permuted test scores and B is the number of permutations.

Best,
Holger 


-------- Original-Nachricht --------
> Datum: Wed, 30 Jan 2008 15:27:25 +0000
> Von: Claus-Dieter Mayer <claus at bioss.ac.uk>
> An: olivier armant <olivier.armant at itg.fzk.de>
> CC: bioconductor at stat.math.ethz.ch
> Betreff: Re: [BioC] SAM siggenes number of permutations

> Dear Oliver,
> 
> my guess is that you have 2 groups with 3 samples each in which case 
> there are only 20 different possible permutations and the software is 
> clever enough to realise that. In that case the calculation is exact, 
> but you will not find anything significant as the smallest possible 
> p-value is 5% (1/20) for a one-sided and 10%  (2/20) for a two-sided 
> test. The problem of how large groupsizes must be in order to apply 
> permutation tests was discussed on this list some time ago, have a look 
> at https://stat.ethz.ch/pipermail/bioconductor/2007-November/020110.html.
> 
> Hope that helps,
> 
> Claus
> 
> olivier armant wrote:
> > Dear all,
> >
> > I try to do SAM on my data using siggenes on R 2.4.1 (I am a beginner)
> >
> > The function I use is (after creating the vector)
> > sam.out<-sam(data.gcrma, sam.c1, B=100, var.equal=TRUE, Set med=TRUE)
> >
> > It seems to work well but I get allways the message:
> >  number of effective permutations=20
> >
> > Does it means that only 20 permutations were done, werheas I ask for 100
> permutations with the function B=100??
> >
> > I read in the SAM excel package from standford that a precise FDR
> requires 1000 permutations!!!What do you think??
> >
> > Help would be welcome
> >
> >
> > Olivier ARMANT PhD.
> >
> > Institute of Toxicology and Genetics
> > Forschungszentrum Karlsruhe
> > Hermann-von-Helmholtz-Platz 1
> > D-76344 Eggenstein-Leopoldshafen
> > Germany
> >
> >  tel: +49-7247-82-2560
> >  fax: +49-7247-82-3354
> >
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> -- 
> ***********************************************************************************
>  Dr Claus-D. Mayer                    | http://www.bioss.ac.uk
>  Biomathematics & Statistics Scotland | email: claus at bioss.ac.uk
>  Rowett Research Institute            | Telephone: +44 (0) 1224 716652
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