[BioC] outlier probes detection

andrea.grilli at ior.it andrea.grilli at ior.it
Wed May 9 10:20:17 CEST 2012

Hi Guido,
thank you for your reply.
I checked the package Harshlight you suggested. Although it detects  
outlier arrays (and not outlier probes) it works well for the case,  
because it gives a percentage of the defects and that's better than a  
simple visual evaluation.
I have one question about the package evaluation of these defects.  
Because of the intense calculation, I tried either splitting the case  
study in two groups (20 and 20 arrays) and later on with the 40 chips  
all together: according to the package output, one array should be  
excluded only in the second case. Is there some sort of evaluation of  
the defects depending also on the set of arrays a chip is analyzed  
with? I flipped through the concerning paper but I didn't find any  
information about that..

I also checked the solution proposed by Okko (thank you for your  
suggestion), but because it's a stronger approach I'll need more time  
to evaluate it.


"Hooiveld, Guido" <Guido.Hooiveld at wur.nl> ha scritto:

> Hi Andrea,
> If the affected area is relatively small (less than 5-10% of total  
> area) we usually ignore these scratches/bubbles (because each  
> probeset is comprised of multiple probes, and the robust  
> summarization methods usually used within RMA (median polish or  
> M-estimator) are able to handle these outliers pretty well).
> Alternatively, the package 'Harshlight' offers options to correct  
> for various types of artefacts.
> http://www.bioconductor.org/packages/2.10/bioc/html/Harshlight.html
> Regards,
> Guido
> ---------------------------------------------------------
> Guido Hooiveld, PhD
> Nutrition, Metabolism & Genomics Group
> Division of Human Nutrition
> Wageningen University
> Biotechnion, Bomenweg 2
> NL-6703 HD Wageningen
> the Netherlands
> tel: (+)31 317 485788
> fax: (+)31 317 483342
> email:      guido.hooiveld at wur.nl
> internet:   http://nutrigene.4t.com
> http://scholar.google.com/citations?user=qFHaMnoAAAAJ
> http://www.researcherid.com/rid/F-4912-2010
> -----Original Message-----
> From: bioconductor-bounces at r-project.org  
> [mailto:bioconductor-bounces at r-project.org] On Behalf Of  
> andrea.grilli at ior.it
> Sent: Tuesday, May 08, 2012 12:15
> To: bioconductor at r-project.org
> Subject: [BioC] outlier probes detection
> Dear all,
> I'm performing an analysis on HGU133plus2 arrays with 40 samples;  
> looking at their surface with "affyPLM" package, I've seen a couple  
> of arrays with small scratches and one more with a small bubble.  
> Because I don't want to exclude these arrays (according to Murphys'  
> law 2 on 3 belong to the class with less samples), I want to detect  
> those probes and to exclude them.
> I was thinking in some outlier detection method, but because I'm new  
> to this problem I don't know if this is the right method and which  
> packages can be appropriate (did some research but I've no clear  
> idea).
> Any help is really appreciated,
> andrea
> Dr. Andrea Grilli
> andrea.grilli at ior.it
> phone 051/63.66.756
> Laboratory of Experimental Oncology,
> Development of  Biomolecular Therapies unit, Rizzoli Orthopaedic  
> Institute Codivilla Putti Research Center via di Barbiano 1/10
> 40136 - Bologna - Italy
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