[BioC] GOstats

[Francois Pepin]

Hi Al,

GOstats depends on the GO package, which is updated at the same time as
the other annotation packages. That happens once per stable release if
I'm not mistaken.

My suggestion would be to update your annotations (e.g. KEGG, hgu95av2
and GO) because they're quite out of date: versions 1.6.5. The current
version for bioC 1.8 is 1.12.0.

Running your query on an up-to-date version of the GO annotation gives
me the following:
> GOTERM$"GO:0031975"@Term
[1] "envelope"

I think you have a mix from different versions, because your Biobase is
version 1.11.17, while the current version for bioC 1.8 is version
1.10.1. Sometimes strange behavior can happen when packages from
different versions are installed.

You can update your annotations using the biocLite 
source("http://www.bioconductor.org/biocLite.R")
and then updating the package that you want:
biocLite('GO')

I strongly suggest that you update all of your annotation packages to
the same version, because code generally breaks when your chip
annotation, for example, points to a KEGG pathway that the KEGG
annotation ignores.

Hope this helps,

Francois

On Tue, 2006-09-12 at 22:43 +0100, Al Ivens wrote: 
> Hi,
> 
> I am trying to use GOstats (1.6.0) for GOSlim analyses, but have just
> realised that several of my selected Slim terms (chosen via AmiGO
> http://www.godatabase.org/) are not in GOstats.
> 
> > GOTERM$"GO:0031975"
> NULL
> > GOTERM$"GO:0007067"
> GOID = GO:0007067
> Term = mitosis
> Definition = The division of the eukaryotic cell nucleus to produce two
> daughter nuclei that, usually, contain the identical chromosome
>      complement to their mother.
> Ontology = BP
> 
> I have tried the text search methods as suggested by Nianhua recently,
> also drew a blank.  The unifying feature of all the "failures" is that
> they have high number GOIDs.  
> 
> Is there a simple way of finding what the highest GOID in GOstats is?
> Also, I guess, when might GOstats be updated!?
> 
> Many thanks,
> 
> al
> 
> > sessionInfo()
> Version 2.3.1 (2006-06-01) 
> i386-pc-mingw32 
> 
> attached base packages:
> [1] "splines"   "tools"     "methods"   "stats"     "graphics"
> "grDevices" "utils"     "datasets"  "base"     
> 
> other attached packages:
>    GOstats   Category   hgu95av2       KEGG   multtest genefilter
> survival     xtable       RBGL   annotate         GO      graph
> Ruuid    Biobase 
>    "1.6.0"    "1.4.1"    "1.6.5"    "1.6.5"   "1.10.2"   "1.11.7"
> "2.28"    "1.3-2"    "1.8.1"   "1.10.0"    "1.6.5"   "1.10.6"   "1.10.0"
> "1.11.17" 
>     gplots      gdata     gtools    lattice       MASS    statmod
> sma      limma      Hmisc 
>    "2.0.2"    "2.0.2"    "2.0.2"  "0.13-10" "7.2-27.1"    "1.2.4"
> "0.5.15"   "2.7.10"   "3.0-12"
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>