Hi guys, I have a question about the normalization of RNA Seq data. I have 3 types of cells of which I would like to identify the differentially expressed genes. As reported in many papers and tutorials, data have to be normalized together. However, I'm afraid that the normalisation could affect the expression of the genes of one of the three groups for some reasons that I do not know perfectly. Is there a way to make the groups comparable after making a normalisation internal to each cell type?
Thank you in advance