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@wur.nl 


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