[BioC] SAM siggenes number of permutations

[Claus-Dieter Mayer]

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
>
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>
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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
 Aberdeen AB21 9SB, Scotland, UK.     | Fax: +44 (0) 1224 715349