[BioC] SAM : warning messages problem

Willy Wynant Willy.Wynant at curie.fr
Mon Mar 15 13:57:12 MET 2004


Hi,

I am using siggenes package and I am encountering problems with warning 
messages with the function sam.

For example, if I type :

res<-sam(data,3:11,12:88,B=1000,alpha.s0=seq(0,1,0.02),factor.s0=1.4826,delta.fdr=(1:10)/10,rand=123,vec.lambda.p0=(0:95)/100,ngenes=NA,iteration=10,initial.delta=(1:20)/10)

I've got as result the SAM analysis and the following answer:

Warning messages :
1:multi-argument returns are deprecated in : 
return(r,s,r.perm,s.perm,Z,mat.samp,var.0.genes,NA.genes)
2:multi-argument returns are deprecated in : 
return(alpha.hat,s.zero,cv,cv.zero)
3:multi-argument returns are deprecated in : return(p0,spline.out,vec.p0)
4:multi-argument returns are deprecated in : return(tab.fdr,mat.fdr,p0)
5 :multi-argument returns are deprecated in : 
return(d,d.sort,s,d.bar,d.perm,mat.samp,s0,FDR,p0,fdr.ngenes,

I installed the R.1.8.1 version.

Could you help me ?

Thank you



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