[BioC] problem with creating array annotation package

[Marc Carlson]

Hi Guido,

So Chinese Hamster is not supported with a schema etc.  I actually have 
plans in the works to generalize things so that organisms that have not 
been supported in the past can start to be supported in this way, but 
1st I have to make the code that generates the org packages more general 
and robust.  You are correct that the problem is that internally the 
code is expecting a schema to be present in AnnotationDbi (and that 
knows based on a field in the metadata which schema to use).  In your 
case, there is no schema and the metadata is pointing to the wrong 
schema as well (and thus also to the wrong org package).

I have an idea for a way you might be able to hack this to make it 
partially functional.  Send me a separate email if you are interested in 
trying this.

   Marc



On 09/09/2013 12:48 PM, Hooiveld, Guido wrote:
> Hi Marc and others,
> I would like to create an annotation package for an microarray, but I am stuck. Could you please advise how to do this?
> - We are analyzing CHO samples on a Chinese Hamster microarray.
> - I have mapped the probesets on the array to corresponding RefSeq IDs.
> - As you may recall, I have created a org.db (org.Cgriseus.eg.db) using the function makeOrgPackageFromNCBI()
> - I am following the vignette / PDF "SQLForge: An easy way to create a new annotation package with a standard database schema."
>
> Problem I face now is which database scheme to use.
> For the well-studied organisms like human, mouse, pig, etc a scheme is available, but for Chinese Hamster that is not the case.
> As test I just used the "MOUSECHIP_DB" database scheme, but this seems not to work; see error below. I *think* this is because under the hood the mouse org.db is accessed, which obviously doesn't have annotation info for Chinese Hamster RefSeq IDs... If so, how then to point to the 'org.Cgriseus.eg.db'?
>
> Any pointers are appreciated!
> Thanks,
> Guido
>
>> head(array.mapping)
>                   V1           V2
> 1 NM_001243976.1_at NM_001243976
> 2 NM_001243977.1_at NM_001243977
> 3 NM_001243978.1_at NM_001243978
> 4 NM_001243979.1_at NM_001243979
> 5 NM_001243980.1_at NM_001243980
> 6 NM_001243981.1_at NM_001243981
>> makeDBPackage("MOUSECHIP_DB",
> +               affy=FALSE,
> +               prefix="CH_Test",
> +               fileName="D:\\CH\\array_mapping.txt",
> +               baseMapType="refseq",
> +               version="1.0.0",
> +               manufacturer = "Affymetrix",
> +               chipName = "Chinese Hamster Array",
> +               manufacturerUrl = "http://www.affymetrix.com")
> baseMapType is refseq
> Error in sqliteExecStatement(con, statement, bind.data) :
>    RS-DBI driver: (error in statement: no such table: src.refseq)
> ---------------------------------------------------------
> Guido Hooiveld, PhD
> Nutrition, Metabolism & Genomics Group
> Division of Human Nutrition
> Wageningen University
> Biotechnion, Bomenweg 2
> NL-6703 HD Wageningen
> the Netherlands
> tel: (+)31 317 485788
> fax: (+)31 317 483342
> email:      guido.hooiveld at wur.nl
> internet:   http://nutrigene.4t.com
> http://scholar.google.com/citations?user=qFHaMnoAAAAJ
> http://www.researcherid.com/rid/F-4912-2010
>
>
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>
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