[BioC] outlier probes detection

[Djork-Arné Clevert]

Hi Andrea,

I'm happy to help you in this issue, just let me know if you need any further 
details regarding the farms algorithm or its assessment.
If I recall correct are the probes of a probe-set spatial distributed over the 
whole HGU133plus2 array surface, so I don't expect that small scratches or 
bubbles have an impact on the farms-summarization as they will affect only 
very few probes within the probe-set. 

Cheers,
Okko

-- 

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e: okko at clevert.de
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Am 09.05.2012 um 10:20 schrieb andrea.grilli at ior.it:

> 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.
> 
> Andrea
> 
> 
> "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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> 
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