[BioC] GOstats and custom annotation problem

[Dario Greco]

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
Building Cultivator II
P.O.Box 56    Viikinkaari 4
FIN-00014    Finland

Office: +358 9 191 58951
Fax: +358 9 191 58952
Mobile: +358 44 023 5780

Lab WebPage:
http://www.biocenter.helsinki.fi/bi/dna-microarray/

Personal WebPage:
http://www.biocenter.helsinki.fi/bi/dna-microarray/dario.htm



On Jan 4, 2007, at 2:08 PM, 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_U 
>> S.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_IDENTI 
>> FICATIO
>> 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