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=1.482 6,delta.fdr=(1:10)/10,rand=123,vec.lambda.p0=(0:95)/100,ngenes=NA,iter ation=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

Hi, please use version 1.0.6 of the siggenes package. You will find this version in the developmental section of Bioconductor. Holger > 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=1.482 6,delta.fdr=(1:10)/10,rand=123,vec.lambda.p0=(0:95)/100,ngenes=NA,iter ation=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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > --

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=1.4 826,delta.fdr=(1:10)/10,rand=123,vec.lambda.p0=(0:95)/100,ngenes=NA,it eration=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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+

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@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=1.482 6,delta.fdr=(1:10)/10,rand=123,vec.lambda.p0=(0:95)/100,ngenes=NA,iter ation=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 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor