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. 

Do you mean, normalize the data from both platforms together?

Basically, you can't.