[BioC] GOstats and custom annotation problem

[Dario Greco]

hi again,
Robert's suggestion

  library("hgu133pEG800")
   hgu133pEG800ENTREZID <- hgu133pEG800LOCUSID

worked fine (of course).

so at the moment, i would say that this is fixed, unless someone  
doesn't want to make AnnBuilder and GOstats fully compatible (maybe  
useful option anyway)... :)

thank you for your kind help.
d

-- 

Dario Greco

Institute of Biotechnology - University of Helsinki
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On Jan 4, 2007, at 7:37 PM, Robert Gentleman wrote:

> 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_U 
>> S.U  
>> TF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.U 
>> TF-  
>> 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