differential expression and meta analysis of microarray
2 answers
You could try these two http://homer.salk.edu/homer/basicTutorial/affymetrix.html
From Data import to Normalization in Microarray Analysis using in R (Part I) Hope it will help.
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I heard about the COMBAT batch correction and cross-platform normalization method then you can merge the datasets by means of common ENTREZ identifiers to obtain common space across all platforms.