[BioC] SAM : warning messages problem

[Robert Gentleman]

Hi,
  It should not be a problem for your analysis. The warning message is
  there to inform the programmer that they are using a technique that
  was allowed (some view it as a bug) but which will be removed from
  some subsequent version of R (probably 1.9.0 - which is due out in a
  month or so).

  We will track down the error and put up a patched version - probably
  later today. Some time tomorrow you could check to see if it is
  there and if so download the new version
  
  Robert

On Mon, Mar 15, 2004 at 01:57:12PM +0100, Willy Wynant wrote:
> 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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> Bioconductor at stat.math.ethz.ch
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| Robert Gentleman                 phone : (617) 632-5250                   |
| Associate Professor              fax:   (617)  632-2444                   |
| Department of Biostatistics      office: M1B20                            |
| Harvard School of Public Health  email: rgentlem at jimmy.harvard.edu        |
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