[BioC] Add new affy organism platform

[James W. MacDonald]

Hi Marc,

My understanding is that you can't use SQLForge to create a chip-level 
.db package unless there is a corresponding db0 package. Is that not 
true? In this case the OP wants a rice.db package - is there an easy way 
to make such a beast without a corresponding db0 package? Perhaps using 
the makeOrgPackageFromNCBI?

Best,

Jim



On 4/29/2013 6:26 PM, Marc Carlson wrote:
> Hi Ekta,
>
> There are many different kinds of annotation packages in 
> Bioconductor.  Which kind did you mean?  A .db package?  A .cdf 
> package?  Maybe something else?
>
> There is a vignette that can help you to make a .db package here 
> called "SQLForge: An easy way to create a new annotation package with 
> a standard database schema.":
>
> http://www.bioconductor.org/packages/release/bioc/html/AnnotationForge.html 
>
>
> If it's a cdf package, then you should probably look here:
>
> http://www.bioconductor.org/packages/release/bioc/html/makecdfenv.html
>
>
> Hope this helps,
>
>
>   Marc
>
>
>
>
> On 04/28/2013 06:49 AM, Ekta Jain wrote:
>>     Dear All,
>>
>>     The affy platform annotation packages available in bioconductor 
>> do not have
>>     "rice" included. Is there a way i can still use this in R?
>>
>>     Any suggestions would be highly appreciated.
>>
>>     Thank you
>>
>>     Ekta Jain
>>
>>     Research Analyst
>>     Biotechnology and Bio-resources Division
>>     The Energy and Resources Institute, India Habitat Centre
>>     Lodhi Road, New Delhi - 110033
>>     #09958818853
>>     [1]ekta.jain at teri.res.in
>>
>>
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>>
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>> Disclaimer:
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>>
>>     1. mailto:ekta.jain at teri.res.in
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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