Hi,

How is it possible that in the similarity matrix resulting from the mgeneSim() function (gene semantic similarity measurement, R package GoSemSIm), there are no 1's on the diagonal ? They are only there when using the measure="Wang" method but for the rest, such as "Resnik", "Rel" etc. there is a value different from 1 ?

library(GOSemSim)
hsGO <- godata('org.Hs.eg.db', ont="MF")
mgeneSim(genes=c("835", "5261","241", "994"),  semData=hsGO,  measure="Rel",verbose=FALSE)

##        835  5261   241   994
## 835  0.947 0.400 0.255 0.488
## 5261 0.400 0.908 0.325 0.462
## 241  0.255 0.325 0.941 0.273
## 994  0.488 0.462 0.273 0.907

An example is taken from

https://yulab-smu.top/biomedical-knowledge-mining-book/GOSemSim.html

So how is the similarity in GoSemSim calculated?

The results are completely different from those provided by the GOSim package and the getGeneSim() function for the same similarity measures (e.g. on the diagonal, the similarity matrix is 1, as you would expect). I was comparing whether the two packages give the same results, but apparently not.