[BioC] outlier probes detection

Wed May 9 11:59:10 CEST 2012

Yes, now I notice that point.
Thank you so much for your help,
Andrea

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

> Hi Andrea,
> I have to admit that it has been a while since I actively used  
> Harshlight. However, AFAIK Harshligt detect both outlier probes. You  
> can have Harslight automatically correct these outlier probes by  
> having their (outlier) value replaced by either 'NA' or by the  
> median value for all arrays.
> See '?Harshlight' for more details: "na.sub: If TRUE, the intensity  
> values of the input affyBatch that are affected by defects will be  
> changed in NA. If FALSE, the values will be substituted with the  
> median of the intensity values of the other chips."
>
> If you have a brief look at Figure 2 of this Harshlight paper  
> http://www.biomedcentral.com/1471-2105/6/294 you will see that a  
> representative image of all arrays is obtained by creating a 'median  
> image'. Each individual array is then compared to this median image,  
> and defects are identified by deviations to the median image using a  
> set of criteria (again see ?Harshlight for more details).
> Thus, the number of arrays that is analysed together will (slightly)  
> affect the outcomes of Harshlight. If I were you I would analyse all  
> arrays from an experiment together (in your case all 40), have  
> Harshlight replace all outlier values by the median, and then  
> continue with normalizing using e.g. (GC)RMA.
>
> HTH,
> Guido
>
> -----Original Message-----
> From: andrea.grilli at ior.it [mailto:andrea.grilli at ior.it]
> Sent: Wednesday, May 09, 2012 10:20
> To: Hooiveld, Guido
> Cc: bioconductor at r-project.org
> Subject: Re: [BioC] outlier probes detection
>
> 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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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