[BioC] problem with list.siggenes in siggenes package

ruma rumas at cdac.in
Mon May 21 09:11:27 CEST 2007


Dear all,

I have trouble using the list.siggenes function in the siggenes package.
When I try using it, I have the following error:
Error in list.siggenes(sam.out, 3, file = "", gene.names = nrow(data)[[1]],
:
        The length of gene.names must be equal to the number of genes.

I know it must be a silly mistake somewhere.. but I'm unable to figure it
out.

I used a dataset of 22622 genes and 40 samples, where the first column lists
the clone ID ad the second column lists the names, continued with the rest
40 samples.
With my original data, I gave the following commands:
>read.matrix(file="sf40.txt",header=TRUE,sep="\t",skip=0)->raw.data
>raw.data->data
>data.cl<-c(rep(1,42))
>sam(data,data.cl,method=d.stat,delta=NULL,n.delta=10,p0=NA,lambda=seq(0,0.9
5,0.05),ncs.value="max",ncs.weights=NULL,gene.names=nrow(data)[[1]],q.versio
n=2)->sam.out
>list.siggenes(sam.out,3.0,file="",order=TRUE,text=NULL,append=FALSE)

Can anyone help me out with the same?

Thanks in advance.
Ruma.



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