[BioC] RNA degradation

[Delphine Fleury]

Dear all,
Thanks for your answer about my design problem.
I have another question about the RNA degradation control of Affy array.

With the Affymetrix software (in the expression report), the controls
indicated there was no RNA degradation in my arrays. But when I analyse
the AffyBatch with R, I have highly significant difference between 5'
and 3' also observed in the RNA digestion plot, so degradation. Can you
explain the difference between the two observations with Affy software
and affy package of Bioconductor ? And which control can I trust ?
Thanks in advance.

Delphine
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Delphine Fleury
DEPARTMENT OF PLANT SYSTEMS BIOLOGY           Fax:32 (0)9 3313809
GHENT UNIVERSITY/VIB,    Technology Park 927, B-9052 Gent, Belgium
Vlaams Interuniversitair Instituut voor Biotechnologie         VIB
mailto:defle at psb.ugent.be                  http://www.psb.ugent.be