[BioC] SAM siggenes number of permutations

Stefano Calza stef at biostatistics.it
Wed Jan 30 16:06:39 CET 2008

How many samples do you have in each group?

You can't get 100 different permutations, with 3 vs 3 comparison (for example)

On Wed, Jan 30, 2008 at 03:56:15PM +0100, olivier armant wrote:
<olivier>Dear all,
<olivier>I try to do SAM on my data using siggenes on R 2.4.1 (I am a beginner)
<olivier>The function I use is (after creating the vector)
<olivier>sam.out<-sam(data.gcrma, sam.c1, B=100, var.equal=TRUE, Set med=TRUE)
<olivier>It seems to work well but I get allways the message:
<olivier> number of effective permutations=20
<olivier>Does it means that only 20 permutations were done, werheas I ask for 100 permutations with the function B=100??
<olivier>I read in the SAM excel package from standford that a precise FDR requires 1000 permutations!!!What do you think??
<olivier>Help would be welcome
<olivier>Olivier ARMANT PhD.
<olivier>Institute of Toxicology and Genetics
<olivier>Forschungszentrum Karlsruhe
<olivier>Hermann-von-Helmholtz-Platz 1
<olivier>D-76344 Eggenstein-Leopoldshafen
<olivier> tel: +49-7247-82-2560
<olivier> fax: +49-7247-82-3354
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Stefano Calza, PhD
Researcher - Biostatistician

*Sezione di Statistica Medica e Biometria
 Dipartimento di Scienze Biomediche e Biotecnologie
 Università degli Studi di Brescia - Italy
 Viale Europa, 11 25123 Brescia
 email: calza at med.unibs.it
 Phone: +390303717653
 Fax: +390303717488

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