Hi Holger
I got an Warning message when I used the data: 

> sam.out = sam(sumis, cl, rand = 123, gene.names = sumis.names, var.equal = 
>TRUE)
We're doing 70 complete permutations
Warning message:
There are 2 variables with zero variance. These variables are removed,
and their d-values are set to NA. 

how serious is this warning, and how can I identify the 2 variables with zero 
variance?
 thanks
Joseph







________________________________
From: Holger Schwender <holger.schw@gmx.de>

Sent: Mon, April 4, 2011 12:09:53 PM
Subject: Re: [BioC] prepare data matrix for siggenes

siggenes does not care about how you call the columns of your matrix. So both 
sam and ebam should work.

Holger


-------- Original-Nachricht --------
> Datum: Mon, 4 Apr 2011 10:57:11 -0700 (PDT)

> An: bioconductor@r-project.org
> Betreff: [BioC] prepare data matrix for siggenes

> I am preparing data matrix for siggenes as follow:
> 
> data=read.table("data.txt", skip=1, header = F)
> data=as.matrix(data)
> data[1:3, ]
> 
>        V1   V2   V3   V4   V5   V6   V7   V8
> [1,] 0.26 0.21 0.37 0.47 0.43 0.35 0.15 0.50
> [2,] 0.21 0.22 0.40 0.40 0.28 0.23 0.17 0.40
> 
> is it ok to have the defualt column names? if not, how can I suppess it
> when I 
> use read.table?
> Thank you 
> Joseph
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> 
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