I have got a 10X 3' scRNA-Seq dataset of two samples. I want to calculate the average expression for each gene from this scRNA-Seq data. Here, there are some challenges in calculating the average expression, which I'm not sure if I've done that correctly.
I started with some QC and removing outlier cells which includes removing cells with a high fraction of Mitochondria and also eliminating all the cells that do not express any genes.
Then for each gene in the gene-barcode matrix, I calculated average expression which I'm not sure if that is a right way to do that or not. Since I can calculate the expression of each gene by sum over all the counts across all the cells and then divided by the number of cells with non-zero counts for that specific gene.
I appreciate any comments in advance.