[BioC] RNA digestion plots

Lawrence Paul Petalidis lpp22 at cam.ac.uk
Thu Nov 20 12:03:20 MET 2003

Hi William
The RNA plots on your site look great to me. I routinely work with tumour
clinical RNA and the slopes are significantly larger than yours even if the
quality of starting RNA appears to be good. You see, RNA quality control
relies heavily on ribosomal RNA quality (peaks). However, I have had samples
with great ribosomal peaks that actually produce RNAdeg plots with a
significant slope 5' to 3'. Its the state of the mRNA that counts and that
seems to be more sensitive to degradation than the ribosomal one. I would be
very happy working with the ones you show on your site.

With kind regards, Lawrence

Lawrence Paul Petalidis
Ph.D. Candidate

University of Cambridge
Department of Pathology

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of William
Sent: 20 November 2003 07:22
To: BioConductor List
Subject: Re: [BioC] RNA digestion plots

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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> Bioconductor at stat.math.ethz.ch
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