Hi, I'm trying to do some line plots of genes of interest from a bunch of old microarray data we have (dye-swaps!). I can go through the workflow fine as recommended in the limma guide, however, I'd really like to generate some lineplots of the expression. We have quite a lot of arrays per group, and it would be nice to generate some graphs of top hits etc (apart from volcano or MA plots). However, the expression data has numerous dye swaps, and when I just graph the genes of interest from the M data, this doesnt take into account the dye flipping so I get some samples up, some down etc. Is there an easy way to correct the M object so it conforms to the dye-swap as indicated in the design file? sorry for the retro question! thanks Simon