I'm running deseq2 to find differentially expressed genes between patients and controls. The problem is that I have many different variables that could have an effect on the expressed genes, such as age, gender, etc. How can I know which is the effect of those variables in the model? I know that normally the model includes all of the variables as covariates, but it can't be that it also includes some bias?
Maybe this is a naïve question, but I'm very new to these kind of analysis.
Thank you very much, Lluc