R help - Nov 2004 - Questions of Significance Analysis of Microarrays(SAM){siggenes}

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

Please ask questions about Bioconductor packages of the authors or on the 
Bioconductor list.

In this case, only the author can tell you why he did not do something.

On Mon, 22 Nov 2004, pcscan wrote:
> 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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>
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
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