I'm using level 3 RSEM normalized data from GDAC Firehose,
I want to compare the expression of an isoform across tumor samples of an cancer by calculating Z-score. so, my question is, to calculate Z-score of an Isoform (X), what should be the reference population & how to calculate the mean & std.dev of that reference population. Like, should i consider the average & std.dev of all isoforms in the library or average & std.dev of only isoform(X) in all tumor samples.
which formula to be considered ?
Z_Score = (expression of X in a tumor sample (s)) - (mean expression of X from all tumor samples (population) / (standard deviation of X of all tumor samples)
Z_Score = (expression of X in a tumor sample (s)) - (mean expression of all isoforms (+73K) from all tumor samples(population) / (standard deviation of all isoforms of tumor samples)