

Hi, I collected dozens of breast cancer GEO datasets (same platform, Affy U133Plus2) and wonder if there is a way to normalize these datasets so I can compare the gene expression levels across all the datasets even though they are from different labs? I think about doing a RMA to all the datasets together first then followed by SVA to correct for batch effect, or doing RMAs dataset by dataset then follwed by mean-scaling. Does any of these make sense? Or what is the best approach? Any suggestion? Thanks a lot for the help! Ying 		 	   		  
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