I am trying to analyse microarray data using the limma package. When I do it at my work computer I get no problems but when I try the same exact pipeline in my computer I see that the green channel is "seen" as red (ie when I use plotDensities(MA) or plotDensities(RG) there are two red lines and no green). In the end, I get a bunch of NAs in the final topTable() filtered by adjPval.
Both computers are Mac, Mavericks OS, and both R and limma are updated to the last available versions. I have no idea of what's going on but I would really appreciate your help to solve it!
Thanks so much for your time.