Given a set of genes, and some hundreds of experiments in different conditions (from TCGA), I want to measure the pairwise correlation of expression of any pair of genes.
So far, I have been using the Pearson correlation, but this measure has some well known limitations. Also, it may be hard to interpret the result of anti-correlated genes.
I am planning to switch to a different metric.
Do someone have some experience with that?
Would you suggest any measure over the others??