[BioC] problem with GO annotation data

[John Zhang]

>Also, I found I cannot use some of function in AnnBuilder, I don't know why?
>I used it because I want to reproduce the result from AnnBuilder.pdf from
>the package review. it always give me error.

It is a name space issue. Try AnnBuilder:::functionName


>
>Best
>
>Shiliang
>
>
>
>
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>[Previously saved workspace restored]
>
>> library(AnnBUilder)
>Error in library(AnnBUilder) : there is no package called 'AnnBUilder'
>> library(AnnBuilder)
>Loading required package: Biobase
>Loading required package: tools
>
>Welcome to Bioconductor
>
>    Vignettes contain introductory material. To view, type
>    'openVignette()' or start with 'help(Biobase)'. For details
>    on reading vignettes, see the openVignette help page.
>
>Loading required package: XML
>Loading required package: annotate
>
>Attaching package: 'annotate'
>
>
>        The following object(s) are masked _by_ .GlobalEnv :
>
>         getGO
>
>Loading required package: RSQLite
>Loading required package: DBI
>> writeAnnData2Pkg
>Error: object "writeAnnData2Pkg" not found
>> getChroLocation
>Error: object "getChroLocation" not found
>>
>
>
>
>On 7/27/06, Nianhua Li <nli at fhcrc.org> wrote:
>>
>> Hi, Shiliang,
>>
>> You were right that AnnBuilder did have a bug. Thanks for the report!
>>
>> The bug is related to Weijun's question:
>>
>> 
http://thread.gmane.org/gmane.science.biology.informatics.conductor/9227/focus=9
232
>> When baseType is "ll", the baseFile can't be parsed correctly because
>> some parsers assume Entrez Gene is at the 3rd column of the base file.
>> Thanks for John's patch, AnnBuilder just quietly converts the base file
>> into three columns when baseType is "ll". So, weijun's problem got
>> solved. Unfortunately, the parser used for "go2probe" mapping assumes a
>> two-column setting for baseType "ll", therefore can't work correctly
>> with the patch.
>>
>> Now the problem has been solved. You can either get the up-to-date
>> AnnBuilder (v 1.11.6) from svn or wait still Saturday noon to download
>> it using biocLite or from website. You can also modify your local source
>> AnnBuilder/R/ABPkgBuilder.R if you are in a hurry:
>> ===================================================================
>> --- ABPkgBuilder.R      (v1.11.5 or before)
>> +++ ABPkgBuilder.R      (v1.11.6)
>>
>> # Map GO ids to probe ids that are directly associated with the GO ids
>> mapGO2Probe <- function(eg, baseMapType){
>> -     if(baseMapType == "ll"){
>> -            parser(eg) <- file.path(.path.package("AnnBuilder"),
>> -                                    "scripts", "GO2ProbeParser4LL")
>> -        }else{
>> -            parser(eg) <- file.path(.path.package("AnnBuilder"),
>> +        parser(eg) <- file.path(.path.package("AnnBuilder"),
>>                                     "scripts", "GO2ProbeParser")
>> -        }
>>         options(show.error.messages = FALSE)
>>         go2Probe <- try(parseData(eg, eg at go, ncol = 3))
>>         options(show.error.messages = TRUE)
>> ====================================================================
>>
>> Also the probe number mismatch is because your base file has duplicated
>> probeset identifiers.
>>
>> help it works this time :)
>>
>> nianhua
>>
>>
>
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084