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

[Marc Carlson]

Hi Dana,

If you used SQLForge, then I would expect that you have a GGa1ENTREZID 
object that is loaded when you load your GGa1.db package?  This is 
probably what goProfyles is looking for.  In any case the data.frame you 
have constructed below is probably not what the software expects.  It 
probably expected a ProbeAnnDbBimap object (try: class(GGa1ENTREZID) ).  
You probably just need to make a copy of the one you have like this:

GGal.dbENTREZID <- GGa1ENTREZID

Which should work if I am correct about you having a GGa1ENTREZID on 
your search path after loading your package?

Hope this helps,

   Marc


On 12/08/2011 04:37 AM, Dana.Stanley at csiro.au wrote:
> Thanks Marc
>
> Sorry for the late reply, I was away for a week. I did use SQLForge to make a (AnnotationDbi) custom  package that I called GGal.db. It works for all I need, like oligo, limma etc, but when I tried to run goProfyles package with GGal.db it was asking for the object "GGal.dbENTREZID' not found"  Because it named the object starting with GGal.db I assumed that the object should be in the database, and since it was not there, I again assumed I should find a way to add it to db. I know it is looking for a file with 2 columns, my platform gene ID vs ENTREZ ID. I thought if I add this table to the sqlite database maybe it would work??? I was probably wrong. Then I thought that I should make an object in R (not in the database) and call it GGal.dbENTREZID. I tried this:
>> GGal.dbENTREZID=read.table("GGal.dbENTREZID.txt", header=TRUE, sep="\t")
>> head(GGal.dbENTREZID)
>             ID ENTREZID
> 1 CLIGG_02786   373854
> 2   RIGG10718   373854
> 3 CLIGG_03262   373886
> 4   RIGG10181   373886
> 5   RIGG10182   373886
> 6 CLIGG_01647   373887
>
> Then the goProfiles did not ask for the object GGal.dbENTREZID but gave me an error:
> Error in mget(probeslist, env = myenvir, ifnotfound = NA) :
>    second argument must be an environment
>
> As usual I tried to google out what this means with no success. I assume I should use something other than read.table to make an object but I could not find instructions in the package. I only know basic R and the packages I need to use, I can use any help or advice in how to proceed.
>
> Thanks
> Dana
>
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