[BioC] GOstats and custom annotation problem

[Dario Greco]

Hi Robert,
thanks for your post.
these are the commands i have used in AnnBuilder:

version<-"1.1.0"
pkgPath<-getwd()
mypkg <- function(pkgPath, version)
{ABPkgBuilder(baseName="hgu133pEG800.txt",baseMapType="ll",pkgName="hgu133pEG800", 
pkgPath=pkgPath,organism="Homo 
sapiens",version=version,author=list(authors="Dario Greco",maintainer="Dario 
Greco <dario.greco at helsinki.fi>"))}
mypkg(pkgPath, version)

after this, i have build and installed the package as root:
R CMD build hgu133pEG800
R CMD INSTALL hgu133pEG800_1.1.0.tar.gz

both these gave normal output.

i will try now to re-assign LOCUSID to ENTREZID, as you suggested.
i will report the output soon.
thank you again,
d



On Thursday 04 January 2007 19:37, 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_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

-- 

Dario Greco

Institute of Biotechnology - University of Helsinki
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