[BioC] R: Degradation plots - Affy package

[Alberto Goldoni]

4.3 RNA degradation plots
The functions AffyRNAdeg, summaryAffyRNAdeg, and plotAffyRNAdeg aid in
assessment
of RNA quality. Individual probes in a probeset are ordered by location
relative to
the 50 end of the targeted RNA molecule.A
ymetrix (1999) Since RNA degradation
typically starts from the 50 end of the molecule, we would expect probe
intensities to be
systematically lowered at that end of a probeset when compared to the 30
end. On each
chip, probe intensities are averaged by location in probeset, with the
average taken over
probesets. The function plotAffyRNAdeg produces a side-by-side plots of
these means,
making it easy to notice any 50 to 30 trend. The function
summaryAffyRNAdeg produces
a single summary statistic for each array in the batch, o
ering a convenint measure of
the severity of degradation and significance level. For an example


this is the explanation of the affy vignette.

Best regards

Dr Alberto Goldoni

Medical Genetics Unit

S. Orsola-Malpighi Hospital

Via Massarenti n.9, Pad 11

40100 Bologna, Italy

Mobile Phone: +39-338-4145970

Fax: +39-051-636-4004

alberto.goldoni at eurogene.org

www.eurogene.org

www.lagem.it


-----Messaggio originale-----
Da: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] Per conto di Jordi
Altirriba Gutiérrez
Inviato: martedì 5 settembre 2006 15.05
A: martin.doherty at gmail.com
Cc: bioconductor at stat.math.ethz.ch
Oggetto: [BioC] Degradation plots - Affy package

Hi Martin,
Could you tell us more information? Which array are you using? How many 
probes have the probeset?
I have seen these plots in the past with the Rat Genome U34 Set.
The idea of the Affy deg plots is that all the arrays have a similar 
behaviour, as in your case. So I would take as acceptable your arrays.
HTH,

Jordi Altirriba
PhD student
Hospital Clinic (Barcelona, Spain)


>Degradation plots that I have done in the past have usually
>produced plots that increase towards the 3' end in a roughly
>uniform manner. I have done this (breast) experiment on a new
>chip which results in the folowing plot:
>
>http://www.redbrick.dcu.ie/~osama/images/RNAdeg.jpg
>
>This seem to be rather strange,as it peaks in intensity before
>the farthest 3' end. Is there any explanation for this or is there
>any documetnation of this happening elsewhere?

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