Hi, in the latest version of siggenes, there is an argument var.equal for sam. So please update your siggenes version, http://www.bioconductor.org/repository/release1.5/package/html/siggene s.html and see ?sam (or more exactly ?sam.dstat) for this and other new arguments. The version you have does a t-test assuming equal variances. Best, Holger > > Dear All: > Significance Analysis of Microarrays(SAM) > > As we know sam do multiple t.test as following > ## Default S3 method: > t.test(x, y = NULL, alternative = c("two.sided", "less", "greater"),mu = > 0, > paired = FALSE, var.equal = FALSE,conf.level = 0.95, ...) > > var.equal: a logical variable indicating whether to treat the two > variances > as being equal. If 'TRUE' then the pooled variance is used to estimate > the > variance otherwise the Welch (or Satterthwaite) approximation to the > degrees > of freedom is used. > > We are curious why sam in package siggenes do not have var.equal option ? > Are there some reason ? > > > sam(data,cl,B=100,balanced=FALSE,mat.samp=NULL,delta=(1:10)/5,med.fdr= TRUE,s > > 0=NA,alpha.s0=seq(0,1,.05),include.s0=TRUE,p0=NA,lambda.p0=1,vec.lambd a.p0=( > 0:95)/100, > > na.rm=FALSE,graphic.fdr=TRUE,thres.fdr=seq(0.5,2,0.5),ngenes=NA,iterat ion=3, > initial.delta=c(.1,seq(.2,2,.2),4),rand=NA) > > Any help is greatly appreciated. > > Sincerely. Liu Yu Ting > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- Geschenkt: 3 Monate GMX ProMail + 3 Top-Spielfilme auf DVD ++ Jetzt kostenlos testen http://www.gmx.net/de/go/mail ++