Hi, I am working with two-colour data generated by Imagene image analysis. I encountered a problem in limma 2.4.9 I try to read in intensity data (according to the User's guide section 4.4) like this: > targets<-readTargets() > targets SlideNumber FileNameCy3 FileNameCy5 Cy3 Cy5 1 1 slide1-g.txt slide1-r.txt mut wt 2 2 slide2-g.txt slide2-r.txt wt mut > files<-targets[,c("FileNameCy3", "FileNameCy5")] > file.path="../quantification/" > myfun<-function(x) as.numeric(x[, "Flag"] < 1) > RG<-read.maimages(files, source="imagene", path=file.path, wt.fun=myfun) Error in read.maimages(files, source = "imagene", path = file.path, wt.fun = myfun) : targets frame doesn't contain FileName column However, calling read.imagene directly works: > RG<-read.imagene(files, path=file.path, wt.fun=myfun) Could this be a bug in imagene 2.4.9? > sessionInfo() R version 2.2.1, 2005-12-20, powerpc-apple-darwin8.4.0 attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" [7] "base" other attached packages: limma "2.4.9" Best, Georg