I'm performing differential gene expression analysis on rnaseq of tumor samples that might have different amounts of immune infiltrate. Tumors are extracted from patients that respond/not respond to immunotherapy
In my lists I found several immune response related genes significantly modulated but i suspect that this could be related to the different amount of immune infiltrate. In order to highlight the genes that are induced by the tumors and not by the different amount of immune cells... it could be appropriate to normalize the raw reads counts (on which is based my analysis) on the basis of CD3 gene?