[BioC] Add new affy organism platform

[Marc Carlson]

On 04/29/2013 04:07 PM, James W. MacDonald wrote:
> 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
>

No unfortunately that's correct.  I had overlooked that he was working 
with rice.  So a chip level package is not currently possible without a 
corresponding .db0.

But he can probably still make an organism level package for rice by 
calling makeOrgPackageFromNCBI() (from the AnnotationForge package).


   Marc



>
>
> 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
>>>
>>>
>>> ------------------------------------------------------------------------------- 
>>>
>>> -----------------------------
>>>
>>> Disclaimer:
>>>
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>>> References
>>>
>>>     1. mailto:ekta.jain at teri.res.in
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>>
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>