Martin

 

I have seen the same picture as you on RAE 230A and 2.0 arrays, where the peak is actually the penultimate probe at the 3'end for all of my arrays in 4 experiments. 

 

Rizwan

 

-----Original Message-----
From: Alberto Goldoni [mailto:alberto.goldoni@eurogene.org] 
Sent: 05 September 2006 14:22
To: 'Jordi Altirriba Gutiérrez'; martin.doherty@gmail.com
Cc: bioconductor@stat.math.ethz.ch
Subject: [BioC] R: Degradation plots - Affy package

 

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@eurogene.org

 

www.eurogene.org

 

www.lagem.it

 

 

-----Messaggio originale-----

Da: bioconductor-bounces@stat.math.ethz.ch

[mailto:bioconductor-bounces@stat.math.ethz.ch] Per conto di Jordi

Altirriba Gutiérrez

Inviato: martedì 5 settembre 2006 15.05

A: martin.doherty@gmail.com

Cc: bioconductor@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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