[BioC] SAM : warning messages problem

[James MacDonald]

This is really only a problem for the package maintainer. Your results
are not affected.

Basically there has been a change in R, and siggenes has not been
modified to account for that change. Right now everything is still
working correctly, you just have a bunch of annoying error messages.

Best,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> Willy Wynant <Willy.Wynant at curie.fr> 03/15/04 07:57AM >>>
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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