Hi 

I'm trying to analyze 8x 60 k Agilent data using the latest version of Bioconductor and Limma in Rstudio (MacOSX, Yosemite). I read in the microarray data using the following commands:

targets<-readTargets("target_RR.txt")
RG<-read.maimages(targets$FileName, source="agilent")
plotDensities(RG)

but when I look at the plot the GREEN channel is NOT plotted at all! 

One month ago, I ran exactly the same commands/script but with an older version of Bioconductor/Limma and BOTH RED and GREEN channels were plotted back then, so it seems that the problem is related to the most recent update of limma...

It seem that my question is also related to this one (http://www.biostars.org/p/129469/) but so far no solution has yet been found.

Thank you for helping!

Regards

Wannes

PS1: I also ran the command on Rstudio in Windows but got exactly the same problem.

PS2: the "target_RR.txt" file looks like this:

ID    Name    FileName    Cy5    Cy3    Target

1    f1    US22502421_253385010016_S01_GE2_107_Sep09_2_2.txt    R    NR    r
2    f2    US22502421_253385010016_S01_GE2_107_Sep09_2_4.txt    R    NR    r
3    f3    US22502421_253385010016_S01_GE2_107_Sep09_1_3.txt    R    NR    r
4    f4    US22502421_253385010016_S01_GE2_107_Sep09_1_1.txt    R    NR    r

Sorry, I introduced this bug when I tried to make the methods dispatching of plotDensities() more "elegant".

I have committed a fix in limma 3.22.6.