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

From: pcscan <s938611_at_mail.yzu.edu.tw>
Date: Mon 22 Nov 2004 - 23:38:08 EST

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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