Dear Gordon,

Thank you for your answer. I'll look further into Agilent array image 
files with limma.

As I said the problem is that i'm not currently reading image from 
Agilent array, but the text data file with marray library and loading it 
into a maData object like this:

maData = read.Agilent(fnames=input , path=NULL, name.Gf = "gMedianSignal", name.Gb = "gBGMedianSignal", name.Rf = "rMedianSignal", name.Rb = "rBGMedianSignal", name.W= NULL, layout = NULL, gnames = NULL, targets = NULL, notes=NULL, skip=NULL, sep="\t", quote="\"", DEBUG=FALSE, info.id=NULL)




> On 06/20/2013 01:11 PM, Gordon K Smyth wrote:
>> 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@sistemasgenomicos.com>
>>> To: "bioconductor@r-project.org" <bioconductor@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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