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:
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!
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