calculating similarity for a large set of genes

[elise625]

I'm trying to calculate a pairwise similarity using mgeneSim for ~15000 entrezgene ids but this is taking way too long. Is there another/faster way I can achieve this?

[llrs]

Which version are you using? In the latest release version (2.4.0) is faster than the previous one (2.2.0), as per this PR.

My estimations are that it should take now less than half the time it took. By "way too long" how much do you mean? Take into consideration that you want to do 15000^2 comparisons ~ 225 millions of comparisons!