Dear Gordon and Mark,
Thank you very much for your answers.

You were right. All my problems came from the way I construct my DGElist
object.
I used DGEList() constructor and It worked perfectly.

I first constructed a DGEList object manually because looking how to test
the first Case study I found a mail from Davis McCarthy (
https://stat.ethz.ch/pipermail/bioc-sig-sequencing/2011-August/002180.html)
describing a way to manipulate and create a DGEList object. It worked fine
so I used it for my own data. I now see some mistakes I did.

Best wishes,

Amos




-- 
Dr Amos Kirilovsky
CEA
Institut de génomique
2 rue Gaston Cremieux
CP 5706 91057 Evry cedex - France
Tel: (33) 01 60 87 25 35

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