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Hello,
I am trying to do differential gene expression studies in different cancer types and have downloaded gene expression data files from two different databases namely GEO database and TCGA data portal. I now want to normalize these two data sets since the platform TCGA used was Agilent244k Custom Gene Expression G4502A_07 and the GEO's platform was Affymetrix Human Genome U133A 2.0 Array. Could please let me know which tools or software should I use to do this normalization. Thanks in advance.