[BioC] RNA degradation... or not?

[Ken Simpson]

Dear Bioconductors, 

I apologise if this is not 100% appropriate for the list.  I have seen
data sets from a couple of experiments lately, each using four MOE430
version 2 chips, in which one chip of the four has a median PM which is a
factor of three or four higher than on the others.  When I do an RNA
degradation plot, the aberrant chip has a big dip at the 3' end (the
others look fine - the mean log PM increases pretty much linearly as you
go 5' -> 3', and they are roughly parallel to each other) .  Is this
really indicative of RNA degradation, or am I misinterpreting or reading
too much into the plot?  It seems counterintuitive that a degraded sample
would produce *higher* intensities.  My collaborators did check their
samples before labelling (using a Bioanalyser) and they all appeared to be
fine, so the cause of the problem would appear to be downstream.  If
anyone else has seen similar behaviour, I'd be most interested to know -
especially if they worked out what the cause was!

Thanks in advance,

Ken

-- 
Dr. Ken Simpson                        
Research Officer, Division of Genetics and Bioinformatics 
The Walter and Eliza Hall Institute of Medical Research   
1G Royal Parade, Parkville, Vic 3050          
Tel: (03) 9345 2628
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