[BioC] SAM : warning messages problem
Robert Gentleman
rgentlem at jimmy.harvard.edu
Mon Mar 15 14:23:52 MET 2004
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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