[BioC] RNA digestion plots

peter robinson Peter.Robinson at t-online.de
Wed Nov 26 00:38:40 MET 2003

I am looking for help in the interpretation of RNA digestion plots. If I have 
understood the recent discussions, then one expects to see a trend from 3' to 
5' in average probe intensity.

I am comparing two sets of experiments done in two different labs. Both were 
done with mgu74av2 chips. 
One set is basically flat with a slight drop at the very 5' end (probe number 
0) and a large drop at the very 3' end (probe number 15), while the other 
shows a slow increase in intensity from the 5' to the 3' end except for a 
drop at the very 3' end (probe 15). 
Does this indicate that the second set may exhibit problems with RNA 

Also, I cannot seem to find the article:

 "L. Cope. Detecting rna degradation using probe level data from 
oligonucleotide expression arrays. Bioinformatics, 2003"

in pubmed. (This article is listed on the bioconductor site.) Could anybody 
point me to a url to get this article (or perhaps a preprint?)

Thank you!

Peter Robinson
Institute of Medical Genetics
Charite University Hospital

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