Hi,

I am analysing 1-color Agilent microarray data and I wonder what is the 
best variable(s) to use among the numerous variables provided by the 
Feature Extraction software from Agilent.
Should I use the "ProcessedSignal", which according to Agilent 
documentation is the signal left after all pre-processing steps have 
been completed and contains the "Multiplicatively Detrended 
BackgroundSubtracted Signal" , or the "BGSubSignal" which equals to the 
feature signal after background subtraction (using a spatial detrend 
algorithm for background correction), or is it better to import the raw 
MeanSignal and BGMeanSignal (or Median Signal) and use the limma package 
to do background  correction (as done in the Agi4x44preprocess package)?
Does anybody have some experience in using these different feature signals ?
Thank you for any help
Christian


-- 

Christian Brière
UMR CNRS-UPS 5546
BP42617 Auzeville
F-31326 Castanet-Tolosan (France)
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E-mail: briere@scsv.ups-tlse.fr <mailto:briere@scsv.ups-tlse.fr>

http://www.scsv.ups-tlse.fr
http://www.gdr2688.ups-tlse.fr <http://www.gdr2688.ups-tlse.fr/index.php>
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