I am analyzing the scRNA-seq data for breast cancer. Here I want to classify the cells into E+ and E- group which is based on the expression level of gene E (cells with low expression of gene E is E- and cells with high expression of gene E is E+). However, there are several members (isoforms) for gene E. I have to combine them to classify the cells. Here I have two plans:
Just simply sum the normalized expression value for these members and classify the cells based on the sum value.
Based on the clustering algorithm, the group of cells which expressed the specific combinational pattern of these members were defined as E+ and the rests were defined as E-.
Do you have any suggestions to my plans? Or do you have other plans?