I want to calculate tissue specificity and have 2 biological replicates for each gene in each tissue. I first removed any genes that have a rpkm below 1.0 and then log2 transformed all remaining rpkm values. My questions are: is it appropriate to get the average (mean) of the 2 log2rpkm values for each gene. Would I be better averaging the raw rpkm values? Should I be including SD or variance?
Thank you. Kenneth