[BioC] outlier probes detection

Hooiveld, Guido Guido.Hooiveld at wur.nl
Tue May 8 13:22:07 CEST 2012

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.


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 

-----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,

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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