I have a custom gene set that I am trying to compute average expression of across a patient list (sample data set below). Simple averaging of expression values across genes to get an average expression value for a gene set isn't the best way for obvious reasons.
I will greatly appreciate any help with a method or statistical analysis that can perform rank (?) based averaging for gene sets. I am well aware of GSEA, GSVA and the likes that give an enrichment score but they also require two condition sets and my data doesn't have that.
Sample data -
Gene1 Gene2 Gene3 ... GeneX Patient 1 10 15 1 ... Patient 2 2 80 5 ... Patient 3 0.5 150 9 ... Patient 4 . . . ...
While searching I found a similar question but it doesn't satisfactory answer my question.
edit - My goal would be to estimate a score to calculate distance between samples set (patients) based on an average expression of average expression of gene in the gene set.