[BioC] SAM siggenes number of permutations

James W. MacDonald jmacdon at med.umich.edu
Wed Jan 30 16:31:17 CET 2008

Hi Olivier,

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??

Yes. A more correct statement would be that the number of combinations = 
20. You evidently have 6 samples, with 3 in each class. There are only 
20 ways you can make two groups of three, so it doesn't matter that you 
requested B=100.

> I read in the SAM excel package from standford that a precise FDR requires 1000 permutations!!!What do you think??

Ideally you want lots of combinations, as the null distribution with 
only 20 combinations will be very discrete. You can either assume that 
you are getting a reasonable null distribution with 20 combinations, or 
you can decide that isn't good enough and make the assumption that the 
genes all follow a Normal-ish distribution and use a parametric method 
(e.g., the limma package).



> 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
> 	[[alternative HTML version deleted]]
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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