[BioC] sam

[Holger Schwender]

Hi,

oh, this is a bug in sam.wilc. It should be substring(gene.names,1,50) and
not substring(gene.neames,1,50). I actually thought that I have removed this
bug. I will immediately fix this bug. But you can still do your analysis
with the Wilcoxon rank sums by using

> sam(data,cl,method="wilc.stat",...)

instead of

> sam.wilc(data,cl,...)

This will work and give you the same results. Another solution would be to
set gene.names=NULL in sam.wilc.

Best,
Holger


> --- Ursprüngliche Nachricht ---
> Von: "D.Enrique ESCOBAR ESPINOZA" <escobarebio at yahoo.com>
> An: bioconductor at stat.math.ethz.ch
> Betreff: [BioC] sam
> Datum: Tue, 21 Jun 2005 07:59:20 -0700 (PDT)
> 
> while i m trying to use
> the new samr
> it happens that i don t really know how many parameters to enter,
> here is an example
> > sam_NMM.output			<-
> + sam.wilc(samOvary_NMM,samOvary_NMM.cl,delta=NULL,n.delta=10,p0=NA,
> +  lambda=seq(0,0.95,0.05),ncs.value="max",ncs.weights=NULL,
> + gene.names=dimnames(samOvary_NMM)[[1]],q.version=1,R.fold=1,
> +  R.unlog=TRUE,na.replace=TRUE,na.method="median",approx50=FALSE,
> + check.ties=TRUE,rand=123)
> Error in substring(gene.neames, 1, 50) : Object "gene.neames" not
> found
> In addition: Warning message:
> There are 1 genes with ties. The ranks of these ties are randomly
> assigned.
> 
> but in any conbination of parameters that i use i always have the
> same
> output:>Error in substring(gene.neames, 1, 50) : Object "gene.neames"
> not found
> In addition: Warning message:
> There are 1 genes with ties. The ranks of these ties are randomly
> assigned.<
> thanks
> 
> --------------------------------------------------
> D.Enrique ESCOBAR ESPINOZA (B.Sc.) 
> http://adn.bioinfo.uqam.ca/~escd07097301/
> ICQ#: 201778618
> -------------------------------------------------
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> Tel:  (514) 523-8398
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