Hi!

I am new in microarray analysis and in using Bioconductor. I need to 
analyse expression data from monocolor Agilent microarrays (105K).  To 
my surprise, for each array (controls as well as treated samples) the 
distribution of intensity data is bi-modal. Furthermore, it seems that 
more than 10% of the genes are differentially expressed between controls 
and treated samples. Therefore, I wonder what is the best method to use 
in such case for between arrays normalization. I was told that median or 
quantile normalization was not adequate. Should  Invariant Set or VSN 
normalization be better, and what are the packages to use for that ?
Thanks for your help

-- 

Christian Brière
UMR CNRS-UPS 5546
BP42617 Auzeville
F-31326 Castanet-Tolosan (France)
tel: +33(0)5 62 19 35 90
Fax: +33(0)5 62 19 35 02
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>
http://www.ifr40.cnrs.fr

 


	[[alternative HTML version deleted]]

