[BioC] GOstats and custom annotation problem

[Robert Gentleman]

Hi,
   It would help if you could give the complete sequence of commands 
that you used.  It is pretty hard for us to guess just what you did.  I 
have just built a custom annotation package and don't see this behavior.

My code looks like:

  ABPkgBuilder(baseName="eSet22.GB",
                  baseMapType="gbNRef",
                  pkgName="ISBOvarianAnnotation",
                  pkgPath=".",
                  organism="Homo sapiens",
                  otherSrc=c( REFSEQ="eSet22.refseq", UG="eSet22.UG"),
                  version="1.0.0",
                  author=list(
                    authors="Robert Gentleman",
                    maintainer="R. Gentleman <rgentlem at fhcrc.org>"
                    )
                  )

so you would need to replace the baseName variable and the otherSrc 
variables (among other things) to what you are going to use.

Also, after using Annbuilder did you build and install the package? 
Using new version numbers as you proceed helps to detect cases where 
things have not gone as expected.


  In any event, why not just go
  library("hgu133pEG800")
   hgu133pEG800ENTREZID <- hgu133pEG800LOCUSID

  and then things should be fine.



best wishes
   Robert


Dario Greco wrote:
> hi Sean,
> as you advised, i have installed AnnBuilder 1.12.0 and re-built the  
> annotation package.
> as a result, it seems that it keeps creating the "LOCUSID" object, as  
> shown by the QCDATA screen.
> 
> hgu133pEG800QCDATA
> $name
> [1] "hgu133pEG800"
> $built
> [1] "Created: Thu Jan  4 15:41:28 2007 "
> $probeNum
> [1] 17663
> $numMissMatch
> [1] "None"
> $probeMissMatch
> [1] "None"
> $probeMapped
>    hgu133pEG800ACCNUM   hgu133pEG800CHRLOC      hgu133pEG800CHR
>                     0                16128                17268
>    hgu133pEG800ENZYME hgu133pEG800GENENAME       hgu133pEG800GO
>                  1787                15757                14133
> hgu133pEG800LOCUSID      hgu133pEG800MAP     hgu133pEG800OMIM
>                 17601                17180                10240
>      hgu133pEG800PATH     hgu133pEG800PMID   hgu133pEG800REFSEQ
>                  3756                16943                17177
> hgu133pEG800SUMFUNC   hgu133pEG800SYMBOL  hgu133pEG800UNIGENE
>                     0                17268                16998
> $otherMapped
>    hgu133pEG800CHRLENGTHS hgu133pEG800ENZYME2PROBE  
> hgu133pEG800GO2ALLPROBES
>                        25                       
> 778                     7748
>      hgu133pEG800GO2PROBE     hgu133pEG800ORGANISM    
> hgu133pEG800PATH2PROBE
>                      5950                         
> 1                      189
>          hgu133pEG800PFAM   hgu133pEG800PMID2PROBE       
> hgu133pEG800PROSITE
>                     13185                    
> 132527                     9246
> 
> and 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.U 
> TF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF- 
> 8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_ID 
> ENTIFICATION=C
> attached base packages:
> [1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
> [7] "datasets"  "base"
> other attached packages:
> AnnBuilder    RSQLite        DBI   annotate        XML    Biobase
>    "1.12.0"    "0.4-1"   "0.1-10"   "1.12.0"   "0.99-8"   "1.12.2"
> 
> is this a compatibility issue between AnnBuilder and GOstats?
> in BioC 1.8 everything worked fine, as GOstats was happy with  
> "xxxLOCUSID" objects.
> 
> any further suggestion?
> 
> thanks again,
> d
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org