Dear all, I am pretty new using this methods so I am sorry if I ask something very simple. I have some issues with cummeRbund. After downloading my cuffdiff data from Galaxy and creating a database with R, I tried to create the graphics. I have 3 treatments and all three are compared in the cuffdiff tables. When I explore the object cuff I get this information: CuffSet instance with: 3 samples 198476 genes 198905 isoforms 198496 TSS 0 CDS 595428 promoters 595488 splicing 0 relCDS

But then I try to plot the density plot and one of my treatments desappear. When I do the volcano plot I have another issue. When compare 1 with 2, everything ok, but when compare 1 with 3 I only get a plot with one point, and when I compare 2 with 3 I get the same plot as 1 compare with 2. I think that cummeRbund is considering two treatments together as one, and comparing with the other, but I don´t know how to separate them. My CuffSet instance indicate that there are 3 samples.

Thanks a lot for your help. Best, Raquel