I am developing a pipeline that is capable of find non DE genes between different microorganisms. For raw read counts normalization i'm using DESeq, which is good for gene expression comparison intra-experiment. My question is: once i have my gene expression values in a given experiment (GSE), how i can normalize them to fit gene expression analysis with another experiment? What are the variables i need to take into account? What is the best method to do it?
Any suggestion is welcome.