[BioC] Agilent arrays: spot quality weights for limma

Wolfgang Huber whuber at embl.de
Wed Feb 3 13:07:00 CET 2010

Dear Guido

In my view, there is little to be gained by removing (or downweighting) 
individual data points (i.e. for particular features on particular 
arrays) compared to the complications incurred.

However, it is often very useful to filter out features that are not 
performing well (or are consistently dim) throughout the experiment. 
That can be achieved, of course, simply by subsetting the NChannelSet of 
RGList object. This topic (independent or 'non-specific' filtering) has 
been amply discussed on this list.

PS your mail did make it to the list, twice.

	Best wishes

Hooiveld, Guido ha scritto:
> Resend; my first mail apparently did not make it to the list..? 
> ------------------------------------------------------
> Dear listers,
> I am new to the anaysis of 2 dye arrays. Currently I am working with an
> Agilent dataset consisting of 15 arrays. I would appreciate if you could
> share your experiences on ways to 'filter' data using spot quality
> weights for use in limma, specifically whether it is smart to filter on
> intensity of the respective channels in relation (or not) to the
> respective background signals.
> In other words, is filtering cq. setting quality weights based on e.g.
> "gIsPosAndSignif" and/or "gIsWellAboveBG" and/or "gIsSaturated", ... (as
> determined by the Feauture Extraction software) wise to do? If so, what
> would be the best criterium/a for filtering?
> I searched the mailing list, but remarkably I only found this post
> https://stat.ethz.ch/pipermail/bioconductor/2005-September/010188.html 
> but this does not fully address my questions.
> Thanks,
> 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 
> internet:   http://nutrigene.4t.com <http://nutrigene.4t.com/>  
> email:      guido.hooiveld at wur.nl 
> 	[[alternative HTML version deleted]]
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Best wishes

Wolfgang Huber

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