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

Holger Schwender holger.schw at gmx.de
Mon Nov 29 16:24:38 CET 2004

```Hi,

in the latest version of siggenes, there is an argument var.equal for sam.

http://www.bioconductor.org/repository/release1.5/package/html/siggenes.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.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
>
> 	[[alternative HTML version deleted]]
>
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>

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