[BioC] Questions of Significance Analysis of Microarrays(SAM){siggenes}

[yzu]

 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.lambda.p0=(
 0:95)/100,
 na.rm=FALSE,graphic.fdr=TRUE,thres.fdr=seq(0.5,2,0.5),ngenes=NA,iteration=3,
 initial.delta=c(.1,seq(.2,2,.2),4),rand=NA)

 Any help is greatly appreciated.

Sincerely. Liu Yu Ting

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