TCGA data clustering

Question

[aUser]

I downloaded RNAseq data from TCGA for LUAD and LUSC and now I wanted to cluster them. For that, I extracted normalized counts (from DESeq2 object) from each project sample independently, and concatenated (cbind) them. I feel that there should be an additional normalization step I need to perform to counter different project variations, but I am unable to figure it out. Anyone can guide me in this direction? I have been searching but I think my keywords are really bad. Thank you.