thank u very much
shan


On Mon, Apr 22, 2013 at 12:57 PM, Marc Carlson <mcarlson@fhcrc.org> wrote:

> Hi Peter,
>
> Maybe this will help you?
>
> http://www.bioconductor.org/**packages/2.12/bioc/vignettes/**
> AnnotationForge/inst/doc/**SQLForge.pdf<http://www.bioconductor.org/packages/2.12/bioc/vignettes/AnnotationForge/inst/doc/SQLForge.pdf>
>
> Almost all of the packages in Bioconductor have vignettes, which you can
> find by navigating to them by using the web site here:
>
> http://www.bioconductor.org/**packages/2.12/BiocViews.html<http://www.bioconductor.org/packages/2.12/BiocViews.html>
>
> And then clicking on their various landing pages.
>
>
> OR you can navigate to them by using help.start() to display the
> documentation for packages that you have installed.
>
>
>   Marc
>
>
>
>
> On 04/22/2013 07:26 AM, James W. MacDonald wrote:
>
>> Hi Peter,
>>
>> On 4/21/2013 10:25 PM, Wang Peter wrote:
>>
>>> source("http://bioconductor.**org/biocLite.R<http://bioconductor.org/biocLite.R>
>>> ");
>>> biocLite("human.db0");
>>> biocLite("AnnotationDbi");
>>> biocLite("AnnotationForge");
>>> library(human.db0);
>>> library(AnnotationDbi);
>>> library(AnnotationForge);
>>>
>>
>> First, this isn't Perl, so adding in extraneous semi-colons isn't
>> necessary.
>>
>>  available.chipdbschemas();
>>>> dir.create("primeview");
>>>>
>>>>  populateDB("HUMANCHIP_DB",**affy=F,prefix="primeview",**fileName="**
>>> primeviewHumanGeneExprs.txt",**metaDataSrc=c("DBSCHEMA"="**HUMANCHIP_DB","ORGANISM"="Homo
>>>
>>> sapiens","SPECIES"="Human","**MANUFACTURER"="Affymetrix","**CHIPNAME"="PrimeView
>>>
>>> Human Gene Expression Array","MANUFACTURERURL"="http**
>>> ://www.affymetrix.com <http://www.affymetrix.com>
>>> "),baseMapType="eg",outputDir=**"primeview");
>>>
>>
>> You are using arguments for makeDBPackage, but calling populateDB. There
>> is no reason that I can think of that you should be using populateDB
>> directly, unless you just want the sqlite database. I have no idea why you
>> are doing things this way - why not just follow the vignette?
>>
>> In addition, about half of your arguments are all caps, and are quoted.
>> There are no all caps arguments for any of the functions you are trying to
>> use, nor are there any quoted arguments in R.
>>
>> I would recommend just following the vignette. Also, IIRC the primeview
>> chip is just a 3'-biased array, so you can probably also set affy = TRUE
>> and have the parsing of the file done automatically.
>>
>> Best,
>>
>> Jim
>>
>>
>>
>>  seed<-new("AnnDbPkgSeed",**Package =
>>>>
>>> "primeview.db",Version="1.0.0"**,PkgTemplate="HUMANCHIP.DB",**AnnObjPrefix="primeview");
>>>
>>> makeAnnDbPkg(seed,file.path("**primeview","primeview.sqlite")**,dest_dir="primeview");
>>>
>>> Error in match(x, table, nomatch = 0L) :
>>> object 'doc_template_names' not found
>>>
>>>> sessionInfo()
>>>>
>>> R version 3.0.0 (2013-04-03)
>>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>>
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.**UTF-8/C/en_US.UTF-8/en_US.UTF-**8
>>>
>>> attached base packages:
>>> [1] parallel stats graphics grDevices utils datasets methods base
>>>
>>> other attached packages:
>>> [1] AnnotationForge_1.2.0 org.Hs.eg.db_2.9.0 RSQLite_0.11.3 DBI_0.2-5
>>> human.db0_2.9.0
>>> [6] AnnotationDbi_1.22.1 Biobase_2.20.0 BiocGenerics_0.6.0
>>>
>>> loaded via a namespace (and not attached):
>>> [1] IRanges_1.18.0 stats4_3.0.0 tools_3.0.0
>>>
>>>
>>>
>>
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>



-- 
shan gao
Room 231(Dr.Fei lab)
Boyce Thompson Institute for Plant Research
Cornell University
Tower Road, Ithaca, NY 14853-1801
Office phone: 1-607-254-1267(day)
Official email:sg839@cornell.edu
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