[BioC] RNA digestion plots

William Kenworthy W.Kenworthy at murdoch.edu.au
Thu Nov 20 08:22:23 MET 2003

RNA plots are something I have also been looking at, but all the
datasets I have access to can be characterised as "good".  Can anyone
supply a (anonymous?) "cel" file of any persuasion that is known to have
been used with degraded RNA?  On larger arrays, I do see a slight slope,
but not any "rolloff" which I think would represent degradation. 

At the present time, I add a "typical" CELfile from another project that
seems good and adding that to the current affybatch and running the
plots.  Currently, they track very well across projects (especially if
normalised) - so a sample "bad one" would be nice just to see what it
looks like!

I have put four plots up at "http://wdk.dyndns.org/rna/rnadeg.html". 
The red and black traces represent samples that I was informed "might"
have been questionable, but they did pass affy's check criteria, the
green trace is from an experiment that was considered good.


On Thu, 2003-11-20 at 13:27, Kevin Dawson wrote:
> Does any one know when to take the RNA digestion plots seriously. On
> hgu133a arrays, these plots always seem to incline from 5' to 3'. Is there
> a certain slope value that sets the good and bad apart?
> Thank you
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