[BioC] GOstats and custom annotation problem

[Dario Greco]

hi,
thanks for your reply.
actually i have tried to build a new package with AnnBuilder 1.11.6 and it 
creates the "LOCUSID" object.
i will try with 1.12.0.
thanks
d


On Thursday 04 January 2007 14:08, Sean Davis wrote:
> On Thursday 04 January 2007 06:56, Dario Greco wrote:
> > dear list,
> > i am trying to run GOHyperG using a custom annotation package created
> > with AnnBuilder.
> >
> > the package is:
> > hgu133pEG800QCDATA
> > $name
> > [1] "hgu133pEG800"
> > $built
> > [1] "Created: Tue Oct 24 15:08:55 2006 "
> > $probeNum
> > [1] 17663
> > $numMissMatch
> > [1] "None"
> > $probeMissMatch
> > [1] "None"
> > $probeMapped
> >   hgu133pEG800ACCNUM   hgu133pEG800CHRLOC      hgu133pEG800CHR
> >                    0                16174                17275
> >   hgu133pEG800ENZYME hgu133pEG800GENENAME       hgu133pEG800GO
> >                 1783                15693                13226
> >  hgu133pEG800LOCUSID      hgu133pEG800MAP     hgu133pEG800OMIM
> >                17601                17185                10116
> >     hgu133pEG800PATH     hgu133pEG800PMID   hgu133pEG800REFSEQ
> >                 3744                16930                16312
> >  hgu133pEG800SUMFUNC   hgu133pEG800SYMBOL  hgu133pEG800UNIGENE
> >                    0                17275                17007
> > $otherMapped
> >   hgu133pEG800CHRLENGTHS hgu133pEG800ENZYME2PROBE
> > hgu133pEG800GO2ALLPROBES 25                      777                    
> > 6612 hgu133pEG800GO2PROBE     hgu133pEG800ORGANISM  
> > hgu133pEG800PATH2PROBE 5090                        1                     
> > 187 hgu133pEG800PFAM   hgu133pEG800PMID2PROBE      hgu133pEG800PROSITE
> > 13171                   128579                     9223
> >
> >
> > when i run GOHyperG, i run into the following error:
> > GOHyperG(sample, lib="hgu133pEG800", what="CC")
> > Error in get(x, envir, mode, inherits) : variable "hgu133pEG800ENTREZID"
> > of mode "environment" was not found
> >
> > it seems that GOHyperG looks for an object like "mypkgENTREZID", while
> > AnnBuilder creates an object named "mypkgLOCUSID".
> >
> > do you have any suggestions for this problem?
> >
> > here is my session info:
> > sessionInfo()
> > R version 2.4.0 Patched (2006-11-03 r39789)
> > i686-redhat-linux-gnu
> > locale:
> > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UT
> >F-
> > 8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC
> >_NA
> > ME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICA
> >TIO N=C attached base packages:
> > [1] "splines"   "tools"     "methods"   "stats"     "graphics" 
> > "grDevices" [7] "utils"     "datasets"  "base"
> > other attached packages:
> > hgu133pEG800      GOstats     Category   genefilter     survival
> > KEGG "1.0.0"      "2.0.4"      "2.0.3"     "1.12.0"       "2.29"
> > "1.10.0" RBGL        graph           GO   AnnBuilder      RSQLite
> > DBI "1.10.0"     "1.12.0"     "1.14.1"     "1.11.6"      "0.4-1"
> > "0.1-10" annotate          XML      Biobase
> >     "1.12.0"     "0.99-8"     "1.12.2"
>
> Is this an AnnBuilder version issue?  It looks like the newest released
> version of AnnBuilder is 1.12.0, whereas your version is 1.11.6 (and we
> don't know what version you used to actually create the annotation
> package).
>
> Sean

-- 

Dario Greco

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