[BioC] GO problems with annaffy

[Jose Duarte]

Paolo

We had this problem before with the version 1.5 of the metadata
packages. See the previous thread in this list:

https://www.stat.math.ethz.ch/pipermail/bioconductor/2004-March/004139.html

The solution for me was upgrading to the devel version of annaffy and
annotate.

Cheers

Jose


On Thu, 2004-04-08 at 23:40, Paolo Sirabella wrote:
> There appears to be a problem (missing object GOBPID2TERM) with the Gene 
> Ontology metadata (1.5.0) in hgu133a and annaffy (R_1.8.1, 
> Bioconductor_last_release).
> Hints or suggestions are welcomed.
> 
> Thank you
> 
> Follows the history of the problem ...
> ___________________________________________________________________________
> 
> > library(annaffy)
> Loading required package: Biobase
> Welcome to Bioconductor
>          Vignettes contain introductory material.  To view,
>          simply type: openVignette()
>          For details on reading vignettes, see
>          the openVignette help page.
>  
> Synching your local package management information ...
>  
>         Note: reposTools can not access /usr/lib/R/library.
>         This will not affect your R session unless you wish
>         to install/update/remove packages from this directory
>   
> Loading required package: GO  # Just installed ver. 1.5.0
> Loading required package: KEGG
> > library(hgu133a)
> > GO()
>  
> 
> Quality control information for  GO
> Date built:  Tue Jan 13 13:48:19 2004
> Mappings found for non-probe based rda files:
>          GOBPCHILDREN found 3751
>          GOBPPARENTS found 8026
>          GOCCCHILDREN found 452
>          GOCCPARENTS found 1363
>          GOGO2LL found 5785
>          GOLL2GO found 36295
>          GOMFCHILDREN found 1376
>          GOMFPARENTS found 7268
>          GOTERM found 16660
>  
> 
> 
> > hgu133a()
>  
> 
> Quality control information for  hgu133a
> Date built:  Wed Jan 14 18:08:05 2004
> Number of probes: 22283
> Probe number missmatch: None
> Probe missmatch: None
> Mappings found for probe based rda files:
>          hgu133aACCNUM found 22283 of 22283
>          hgu133aCHRLOC found 19717 of 22283
>          hgu133aCHR found 21080 of 22283
>          hgu133aENZYME found 2234 of 22283
>          hgu133aGENENAME found 21130 of 22283
>          hgu133aGO found 14590 of 22283
>          hgu133aGRIF found 9806 of 22283
>          hgu133aHGID found 19257 of 22283
>          hgu133aLOCUSID found 21481 of 22283
>          hgu133aMAP found 20993 of 22283
>          hgu133aNM found 19600 of 22283
>          hgu133aNP found 19600 of 22283
>          hgu133aOMIM found 14283 of 22283
>          hgu133aPATH found 3114 of 22283
>          hgu133aPMID found 20409 of 22283
>          hgu133aSUMFUNC found 1293 of 22283
>          hgu133aSYMBOL found 21130 of 22283
>          hgu133aUNIGENE found 20620 of 22283
> Mappings found for non-probe based rda files:
>          hgu133aENZYME2PROBE found 615
>          hgu133aGO2ALLPROBES found 4680
>          hgu133aGO2PROBE found 3459
>          hgu133aPATH2PROBE found 122
>          hgu133aPMID2PROBE found 52622
>  
> > probeids<-ls(hgu133aSYMBOL)
> > length(probeids)
> [1] 22283
> > probeids.gos<-aafGO(probeids[1:50],"hgu133a")
> Error in exists(num, GOBPID2TERM) : Object "GOBPID2TERM" not found
> 
> ______________________________________________________________________
> 
> -----------------------------
> Paolo Sirabella, PhD
> University of Rome "La Sapienza"
> Dept. of Human Physiology and Pharmacology
> Building of Human Physiology
> P.le Aldo Moro, 5 - 00185 - Roma - Italy
> Tel. ++39 06 49910879
> Fax  ++39 06 233203640
> Email paolo.sirabella at uniroma1.it ; psirab at inwind.it
> Web http://w3.uniroma1.it/cisb/Cisb/members/sirabella
> 
> Res Non Verba
> 
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-- 
Jose Duarte <jose.duarte at anat.ox.ac.uk>