Dear Guido, Thanks for the reminder. A bug fix for genas() has been included in limma 3.18.4, so that genas() now handles vector df.prior in a graceful manner. Best wishes Gordon > Date: Wed, 27 Nov 2013 14:30:08 +0000 > From: "Hooiveld, Guido" <guido.hooiveld at="" wur.nl=""> > To: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> > Subject: [BioC] limma - genas: unexpected warnings > > Hi Gordon, > I am using the function genas() on a model that has been fitted with the > option robust=TRUE. Unexpectedly cryptic warnings are thrown, that are > absent when robust=FALSE. Although this is not an error, I thought you > may want to know. I checked that it is not dependent on my specific > dataset. > > Regards, > Guido > > Using the code from the genas() help page: > ... > ... > # fit a linear model > fit <- lmFit(y,design) > fit2 <- eBayes(fit) > >> genas(fit2, coef=c(2,3), plot=TRUE, subset="F") > $technical.correlation > [1] 0.5 > > $covariance.matrix > [,1] [,2] > [1,] 4.516257 -3.770552 > [2,] -3.770552 4.446184 > > $biological.correlation > [1] -0.8414376 > > $deviance > [1] 114.4627 > > $p.value > [1] 1.031906e-26 > > $n > [1] 210 > > There were 50 or more warnings (use warnings() to see the first 50) >> warnings() > Warning messages: > 1: In if (d0 == Inf) d0 <- 999 * d[1] : > the condition has length > 1 and only the first element will be used > 2: In if (d0 == Inf) d0 <- 999 * d[1] : > the condition has length > 1 and only the first element will be used > 3: In if (d0 == Inf) d0 <- 999 * d[1] : > the condition has length > 1 and only the first element will be used > 4:etc, etc > >> sessionInfo() > R version 3.0.2 Patched (2013-11-10 r64185) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] splines stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] ellipse_0.3-8 statmod_1.4.18 limma_3.18.3 >> > > --------------------------------------------------------- > Guido Hooiveld, PhD > Nutrition, Metabolism & Genomics Group > Division of Human Nutrition > Wageningen University > Biotechnion, Bomenweg 2 > NL-6703 HD Wageningen > the Netherlands > tel: (+)31 317 485788 > fax: (+)31 317 483342 > email: guido.hooiveld at wur.nl > internet: http://nutrigene.4t.com > http://scholar.google.com/citations?user=qFHaMnoAAAAJ > http://www.researcherid.com/rid/F-4912-2010 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}