The thing is, the GNF chip was annotated a few years ago, and will probably not be updated. They did annotate multiple sources though, such as Entrez gene, Unigene, RefSeq, etc. And many of these have multiple ids for each probe. For affy type chips (and others), many probes _will_ actually map to multiple genes (not only multiple transcripts), so I wanted to be sure of what SQLforge was doing exactly. Although for most cases it should definitely be good enough as it is, I don't see why it should be limited to only pass annotation from the first gene that is mapped.

In post-processing, you can always decide what to do with probes that map to multiple genes, but the way it stands, you might simply not realize when this occurs...

Cheers,

Cei

Marc Carlson <mcarlson@fhcrc.org> wrote: 
> Sean Davis wrote:
> > On Mon, Jul 14, 2008 at 12:07 PM, Cei Abreu-Goodger <cei@sanger.ac.uk> wrote:
> >   
> >> Hi Sean,
> >>
> >> Ok, so my example was even worse than I thought. And I had forgot to mention
> >> that the otherSrc parameter wasn't what I needed. So, to return to my bad
> >> example, I now have two separate files, the first column in the first file,
> >> the second in the second file:
> >>
> >>     
> >>> refseqs <- "gnf1m.test.tab"
> >>> refseqs2 <- "gnf1m.test2.tab"
> >>>
> >>> read.table(refseqs)
> >>>       
> >>              V1        V2
> >> 1   gnf1m00050_at NM_008929
> >> 2 gnf1m00051_a_at NM_007487
> >> 3 gnf1m00052_a_at NM_178939
> >> 4 gnf1m00053_a_at NM_181666
> >> 5 gnf1m00054_a_at NM_026430
> >> 6 gnf1m00055_a_at NM_029916
> >> 7 gnf1m00056_a_at NM_181666
> >>     
> >>> read.table(refseqs2)
> >>>       
> >>              V1        V2
> >> 1   gnf1m00050_at NM_172283
> >> 2 gnf1m00051_a_at NM_172283
> >> 3 gnf1m00052_a_at NM_172283
> >> 4 gnf1m00053_a_at NM_172283
> >> 5 gnf1m00054_a_at NM_172283
> >> 6 gnf1m00055_a_at NM_172283
> >> 7 gnf1m00056_a_at NM_172283
> >>
> >> I now add the second file as an otherSrc:
> >>
> >>     
> >>> makeMOUSECHIP_DB(affy=FALSE, prefix="test", fileName=refseqs,
> >>> baseMapType="refseq", otherSrc=c(refseqs2),
> >>>       
> >>                outputDir=".", version="0.9", manufacturer="GNF-Affymetrix",
> >> chipName="gnf1m")
> >>
> >>
> >> But this till doesn't add the second gene's annotation to all the probes
> >> (the resulting package's annotation is exactly the same as in the first
> >> case). Is there any other way?
> >>     
> >
> > I think that the way SQLForge works now, it will only use the
> > additional annotation if the first ID is not successfully mapped.
> > (Someone else should probably confirm my assertion about this).  Since
> > it appears that your first column contains all RefSeq IDs, you will
> > never get to the second column.  So, in short, I don't know how to
> > make SQLForge do what you want.
> >
> > Sean
> >
> >   
> 
> Hi Guys,
> 
> Sean is correct about the purpose of the the otherSrc parameter, and 
> about the way that SQLforge currently works.  The thing that has me 
> scratching my head is why you would want to map multiple genes onto a 
> single probe in your annotation package?
> 
>     Marc

