[BioC] question about SAM R package

[Jianping Jin]

Hi James,

try:
 data=list(x=x,y=y, 
geneid=as.character(1:nrow(x)),genenames=paste("g",as.character(1:nrow(x)),sep=""), 
logged2=TRUE)

see what happens.

JP-

--On Wednesday, October 04, 2006 6:41 PM -0700 James Anderson 
<janderson_net at yahoo.com> wrote:

> Hi,
>   Has anybody used the SAM R package? I followed the pdf of the
> instruction and try to use the examples on the pdf file to test the code.
> However, I am having a problem with running the code, below is the code I
> am running:
>
>
> library(samr)
> set.seed(100)
>
> x<-abs(matrix(rnorm(1000*20),ncol=20))
> dd<-sample(1:1000,size=100)
> u<-matrix(2*rnorm(100),ncol=10,nrow=100)
> x[dd,11:20]<-x[dd,11:20]+u
> y<-c(rep(1,10),rep(2,10))
> data=list(x=x,y=y,geneid=as.character(1:nrow(x)),genenames=paste("g",as.c
> haracter(1:nrow(x)))) samr.obj = samr(data, resp.type="Two class
> unpaired", nperms=100)
>
> I don't have any problem until the last line, when I was running the last
> line, it complains:
>
> perm= 1
> Error in if (logged2) { : argument is of length zero
>
> I don't know what's wrong, I copied the code from the pdf file and run
> it. It supposed to run. Does anybody know how to solve this problem?
>
>   Many thanks,
>   James
>
>  		
> ---------------------------------
>
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>
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##################################
Jianping Jin Ph.D.
Bioinformatics scientist
Center for Bioinformatics
Room 3133 Bioinformatics building
CB# 7104
University of Chapel Hill
Chapel Hill, NC 27599
Phone: (919)843-6105
FAX:   (919)843-3103
E-Mail: jjin at email.unc.edu