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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