[BioC] GO problems with annaffy

[Paolo Sirabella]

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 ...
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> 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

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-----------------------------
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

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