[BioC] (pack: GOSemSim) NA semantic similarities between gene clusters

[Manuel A.Alonso Tarajano [guest]]

Dear all,

I'm using GOSemSim for computing semantic similarities (semsim) between clusters of genes.

The Problem:
I'm obtaining semsim==NA when comparing clusters of genes from which I actually expect a value (i.e. semsim != NA).

However, if I compute semsim between individual genes (present in the analyzed clusters) I obtain semsim values != NA.
For computing semsim between clusters, GOSemSim computes the pairwise semsim between the GO terms present in each of the clusters. Therefore I would expect that, if for at least one pair of genes (one from each cluster) is possible to compute a semsim != NA, then the semsim between the two clusters should also be different from NA.

Is this situation a problem of GOSemSim or is there a wrong assumption from my side?

Thanks a lot in advance for your time,

Manuel

PS:
GOSemSim version:
Ver. 1.8.3 (as from the DESCRIPTION file in the installation folder).
This version is the one currently available in Bioconductor.
source("http://bioconductor.org/biocLite.R")
biocLite("GOSemSim")



 -- output of sessionInfo(): 

Code Examples:

library("GOSemSim")
library(GO.db)
library(org.Hs.eg.db)

clust_as <- c("10603","3551","8470","8915","5295","5518","2810","7534","5591","2887","51177","57630")
clust_r1 <- c("23761")
clust_r2 <- c("30835")
clust_r3 <- c("54332")

# Comparing clusters
> clusterSim(clust_as, clust_r1, ont="BP", organism="human", measure="Resnik", combine="rcmax.avg", drop="NULL")
[1] NA
> clusterSim(clust_as, clust_r2, ont="BP", organism="human", measure="Resnik", combine="rcmax.avg", drop="NULL")
[1] NA
> clusterSim(clust_as, clust_r3, ont="BP", organism="human", measure="Resnik", combine="rcmax.avg", drop="NULL")
[1] NA

# Comparing individual genes (the first one from each cluster)
> geneSim("10603", "23761", ont="BP", organism="human", measure="Resnik", combine="rcmax.avg", drop="NULL")
[1] 0.11
> geneSim("10603", "30835", ont="BP", organism="human", measure="Resnik", combine="rcmax.avg", drop="NULL")
[1] 0.176
> geneSim("10603", "54332", ont="BP", organism="human", measure="Resnik", combine="rcmax.avg", drop="NULL")
[1] 0.266


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