[BioC] how to add a table to AnnotationDbi sqlite database?

[Marc Carlson]

Hi Dana,

I want to help you, but I need to know a lot more information before I 
can do so.  So please excuse me while I ask you a ton of questions:  
What is your sessionInfo?  Do you have a reproducible code snippet for 
us?  Have you read the posting guide here?

http://www.bioconductor.org/help/mailing-list/posting-guide/

What is Gga1?  Is this a database you made from scratch?  Did you 
generate it using AnnotationDbi?  When you said "goProfyles " did you 
mean that you are actually using the goProfiles package?  Assuming you 
are, the error you describe sounds like goProfiles is looking for a 
bimap object, which means you need an annotation package.  If so, have 
you read the vignette called "SQLForge: An easy way to create a new 
annotation package with a standard database schema." from 
AnnotationDbi?  You can find that here BTW:

http://www.bioconductor.org/packages/release/bioc/html/AnnotationDbi.html


   Marc



On 11/30/2011 05:18 PM, Dana.Stanley at csiro.au wrote:
> Hi all
>
> I am trying to use goProfyles with my custom chicken database GGal.db. The package is looking for the file in my database that does not exist :
>
> Error in eval(expr, envir, enclos) : object 'GGal.dbENTREZID' not found
>
> I can make a simple table linking my ID and entrez id that the package is looking for, but I could not figure out how to add it to the database...
> To all of you reading posts and helping others a big THANKS.
>
> Dana
>
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>
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