[BioC] Normalize background on marray Agilent object

[Gordon K Smyth]

Dera Guillermo,

The usual process is to (1) background correct the foreground intensities 
with respect to the background, then (2) normalize the M-values 
(log-ratios).

For an Agilent two colour array, I do this by:

   library(limma)
   RG <- read.maimages(files, source="agilent")
   RGb <- backgroundCorrect(RG, method="normexp")
   MA <- normalizeWithinArrays(RGb, method="loess")

although it is sometimes a good idea to remove positive control probes 
before the normalization step.

A recent example using this pipeline is:

   http://www.biomedcentral.com/1471-2105/14/165

Best wishes
Gordon

> Date: Wed, 19 Jun 2013 22:38:34 +0200
> From: Guillermo Marco Puche <guillermo.marco at sistemasgenomicos.com>
> To: "bioconductor at r-project.org" <bioconductor at r-project.org>
> Subject: [BioC] Normalize background on marray Agilent object
>
> Hello,
>
> I'm currently trying to normalize rBG values for a marray object.
> Data origin is Agilent dual channel array. I've loaded information with
> readAgilent() function.
>
> What's the correct way to normalize the data? I would like to normalize
> background information first maNorm function manual isn't very
> clarifying for me.
>
> Thanks !
>
> Best regards,
> Guillermo.


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