In my understanding, applying size factor to raw count by
scater::normalize() is one type of between-sample normalization. Thus the expression within the same gene are comparable among different sample/cells. However, the size factor seems to doesn't account for gene length effect like TPM, so it should not to use it to do a expression level comparision between different genes, even within the same sample/cell. I was wondering that do I understand right ? If that is right, how to compare expression level between two genes, especially for droplet-based data without TPM value for each genes ?