[BioC] down-weighting control probes in limma (with Agilent arrays)?

[Maciej Jończyk]

> I have a question regarding what weighting function to use when 
> analyzing Agilent data with limma. My
> question is whether or not it makes sense to down-weight the control 
> probes?
>
>
> As far as I can see, the normalization methods don't make explicit 
> use of the control probes and hence I would
> think it would be a good idea to down-weight them. Any opinions on 
> this?
>
> Are there any way to make use of the controls?

Hi Daniel,

Control probes are useful in quality control and normalization steps. 
Of course it depends
on type of control (print, positive, negative,...).
Limma provides several normalization methods, two of them (as I 
remember) uses control probes. You can find
appropriate references in Limma Users Guide.

Weighting function are useful if you want to downweight probes with 
quality issues (e.g. flagged as bad or with low-quality signal,
as defined in weighting function).

In my opinion downweighting control probes (just because they are 
controls) are pointless.

HTH

-- 
Maciej Jonczyk,
Department of Plant Molecular Ecophysiology
Faculty of Biology, University of Warsaw
02-096 Warsaw, Miecznikowa 1
Poland



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