Dear all,
 
I have some questions that I would like to pose to this list.
 
When I normalize microarray data (usually with the methods in normalizeWithinArrays function in limma package) I decrease the correlation between the M values of my replicate arrays. This obviously has an explanation bacause if we normalize "within" arrays, the differences between them tend to become larger. Therefore, if the correlation between replicates decrease, it seems like if we normalize our data we would get "worse" data. 
 
Is this true? Does it happen the same to you? And how do you deal with that?  
 
 

Med venlig hilsen / Regards

João Fadista
Ph.d. studerende / Ph.d. student


 	
 	 AARHUS UNIVERSITET / UNIVERSITY OF AARHUS	
Det Jordbrugsvidenskabelige Fakultet / Faculty of Agricultural Sciences	
Forskningscenter Foulum / Research Centre Foulum	
Genetik og Bioteknologi / Dept. of Genetics and Biotechnology	
Blichers Allé 20, P.O. BOX 50	
DK-8830 Tjele	
 	
Tel:	 +45 8999 1900	
Direct:	 +45 8999 1900	
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E-mail:	 Joao.Fadista@agrsci.dk <mailto:Joao.Fadista@agrsci.dk> 	
Web:	 www.agrsci.dk <http://www.agrsci.dk/> 	
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