Hi all,
 
I have 21 HGU133plus2 affy arrays with widely varying RNA deg slopes
(from 4 to 9.5). Some of the samples are as old as 20 years, some are
much younger. At the moment, the resultant normalized data is very
noisy, and detecting significant differences between the 2 treatments is
difficult. Our hypothesis is that differential RNA degradation is in
part responsible for this. 
 
We have been tossing around the idea of correcting for RNA degradation,
at the individual probe level, using the slope and the distance from the
3' end. Has anyone tried this? Any ideas on whether RMA/ GCRMA
normalization would make this procedure unnecessary?
 
Any input would be much appreciated,
 
Tarun Nayar
Genome Sciences Centre
Vancouver, Canada

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