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@wur.nl internet: http://nutrigene.4t.com http://scholar.google.com/citations?user=qFHaMnoAAAAJ http://www.researcherid.com/rid/F-4912-2010 [[alternative HTML version deleted]]