Linear regression is used in cell type decomposition (TIMER or CIBERSORT). I am wondering if the linearity assumption met during modeling.
I imagine raw count is not eligible because different library size causes non-linearity. Log-transformed value probably cause non-linearity as well, right? So is there any kind of normalization may fit the linear assumption?
Beside, unlike microarray, RNA-Seq library is 0-sum game which is non-linearity (although I don't why this cause non-linearity. This may cause some sort of dependency but the overall expression is still the weighted sum of expression of its conponent, right?)