[BioC] Questions of Significance Analysis of
Microarrays(SAM){siggenes}
yzu
s938611 at mail.yzu.edu.tw
Thu Nov 25 12:44:11 CET 2004
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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