Hi,

As you reported that you are using GOSemSim version 1.8.3, that means you
are using Bioconductor 2.7. The current release of Bioconductor is 2.10,
please update your R and Bioconductor.

Please read the vignette of GOSemSim before you using it, the clusterSim
accept gene lists, not vectors.

Best Regards!
Guangchuang Yu
--~--~---------~--~----~------------~-------~--~----~
Department of Biochemistry & Molecular Biology
College of Life Science and Technology
Jinan University, 601 Huangpu Ave. W.
Guangzhou 510632,  P.R. China
Tel: +86-20-85222677
Email: guangchuangyu@gmail.com
          guangchuangyu@jnu.edu.cn
Publications: http://bit.ly/IpzxpH
-~----------~----~----~----~------~----~------~--~---


On Tue, Jul 24, 2012 at 4:08 PM, Manuel A.Alonso Tarajano [guest] <
guest@bioconductor.org> wrote:

>
> 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
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>

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