[BioC] Normalization of exon arrays with expected global RNA degradation

[ekspiulo]

Hello List,

I'm considering alternate means to normalize an Affy Exon array 
experiment of triplicate arrays over (non) induction of a condition and 
(non) treatment in-vitro with an exoribonuclease.  The same quantity of 
RNA was selected for each array; however, we expect that there will be 
some global or nearly global degradation of transcripts to a small 
degree and many partially degraded transcripts among various of the 4 
samples, and I'm looking to identify those transcripts which were 
partially degraded in one sample compared to another.

I don't think RMA is appropriate for this dataset given that there 
shouldn't be much real up or down regulation; however, there should be 
some extremely common degradation effects in some of the samples.

What normalization approach might be useful here?


Sincerely,

Brian Kennedy
Department of Molecular Cellular Biology
The Ohio State University