[BioC] RNA degradation problem

[fhong@salk.edu]

Dear list,

I have this 8 affy arrays under 2*2 factorial design, with duplicates
under each condition. The RNA degradation plot worries me since the slopes
from 8 arrays are so different, with duplicates under each condition as
one group (see the QC plots at http://cactus.salk.edu/temp/QC-1.jpeg)
I would suspect that these arrays were processed  under different levels
if amplification.

My problem is how to handle this data set beside doing the normalization?
Will this pattern seriously bias the result? I read some previous message
about this topic, just hope to get more information.

Many thanks!
Fangxin


--------------------
Fangxin Hong  Ph.D.
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu
(Phone): 858-453-4100 ext 1105



--------------------
Fangxin Hong  Ph.D.
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu
(Phone): 858-453-4100 ext 1105