>Date: Thu, 1 Dec 2005 18:44:24 +0100 >From: "Dr. D. P. Kreil" <dpkreil at="" gmail.com=""> >Subject: [BioC] limma: semi-bug (?) report for toptable >To: bioconductor at stat.math.ethz.ch > >Dear limma-maintainer, > >Firstly, thank you for providing limma, it has helped our work a lot. > >Now, I am not sure whether this is the right address for this observation. >I noticed that when calculating only one contrast, e.g., > >design2<-model.matrix(~ -1 + tgt); >cont.matrix<-makeContrasts(PvsC=tgtpedicel-tgtcapitellum, levels=design2); >fit2<-lmFit(eset,design2); >cfit2<-contrasts.fit(fit2,cont.matrix); >cfit2.eb<-eBayes(cfit2); > >that this single contrast cannot be named in topTable: > >topTable(cfit2.eb,coef=1); # works >topTable(cfit2.eb,coef="PvsC"); # **broken** > >giving > >Error in toptable(fit = fit[c("coefficients", "stdev.unscaled")], coef = >coef, : > subscript out of bounds > >when a second contrast is added to cont.matrix, the problem disappears. > >I suspect that this is caused by a one-column matrix being implicitly >converted to a vector by R somewhere in toptable. > >While it is easy to work around the problem and one will probably only >encounter it in rare situations, stumbling over it can confuse amd so I >wanted to point out the issue. > >Yours sincerely, > >David. >(Boku University, Vienna) Dear David, It is an issue which is caused, as you suspect, by a one-column matrix being converted to a vector by matrix multiplication. Thanks for pointing it out. Best wishes Gordon