Degradation plots - Affy package
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@martin-doherty-1751
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@jordi-altirriba-gutierrez-682
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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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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 Guti?rrez Inviato: marted? 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? _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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