[BioC] error in limma read.maimages(files, source="imagene")

[Georg Otto]

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