[BioC] GOstats and custom annotation problem

[Sean Davis]

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.UTF-
>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_IDENTIFICATIO
>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