[BioC] DEGseq example in documentation

[Sonja Althammer]

Hello,
I have a problem to reproduce the plots from the example in chapter 5 of the
tutorial:
http://www.bioconductor.org/packages/2.6/bioc/vignettes/DEGseq/inst/doc/DEGseq.pdf

To make sure I have the right installation, I installed bioconductor from
scratch as explained here:
http://www.bioconductor.org/install/

I ran the attached script and get the attached plots. Could anyone tell me
why my plots are different from those in the tutorial? I am wondering if I
am doing sth. wrong?

Any comment would be very helpful!
Thanks in advance!
Sonja