[BioC] SQLForge and probes that map to multiple genes

[Marc Carlson]

Sean Davis wrote:
> On Mon, Jul 14, 2008 at 12:07 PM, Cei Abreu-Goodger <cei at 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