[BioC] problem with list.siggenes in siggenes package

Holger Schwender holger.schw at gmx.de
Mon May 21 12:01:21 CEST 2007

Hi Ruma,

the problem starts in the call of the sam function itself. data is only allowed to consist of the data from the samples (I wonder why you didn't get an error when calling sam.) So you actually should do the following

> data <- raw.data[,3:42]
> cl <- rep(1,40)
> rownames(data) <- raw.data[,2]  

or if you would like to have the clone ids as names

> rownames(data) <- raw.data[,1]

And then use these specifications in sam.

Now to the list.siggenes problem: gene.names must be a vector containing the gene names, but nrow gives you the number of rows data has. You get the names of the differentially expressed genes by

> list.siggenes(sam.out, 3, gene.names=rownames(data))

However, since the gene names are already specified in data (namely by the row names of this matrix), you do not have to specify gene.names. So

> list.siggenes(sam.out, 3)

should be enough.


-------- Original-Nachricht --------
Datum: Mon, 21 May 2007 12:41:27 +0530
Von: "ruma" <rumas at cdac.in>
An: bioconductor at stat.math.ethz.ch
Betreff: [BioC] problem with list.siggenes in siggenes package

> 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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