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 (i.e. when I use
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
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.