[BioC] mouse4302.db and can't find gene symbol annotation

[Andrew Yee]

Thanks for the information, that's extremely helpful.

Thanks,
Andrew

On Tue, Oct 23, 2012 at 10:43 AM, James W. MacDonald <jmacdon at uw.edu> wrote:
> Hi Andrew,
>
>
> On 10/22/2012 10:58 PM, Andrew Yee wrote:
>>
>> I know I've raised a similar issue in May 2009 concerning how
>> frequently the annotation packages are updated, and I imagine this
>> issue has been raised by others as well:
>>
>> For this probe set id, 1449880_s_at, I am having some difficulty
>> finding annotation information for it in the mouse4302.db.
>>
>> The Affymerix website has its gene symbol annotation as Bglap, and the
>> date of their annotation file is from July 2011
>>
>>
>> https://www.affymetrix.com/analysis/netaffx/fullrecord.affx?pk=MOUSE430_2:1449880_S_AT#a_grade
>>
>> However, I can't seem to find a similar annotation in the mouse4302.db
>> annotation package.  I was wondering if there was a simple explanation
>> for this, or perhaps I am doing something wrong.
>
>
> It's a simple explanation. This probeset targets multiple genes, and the
> default of the annotation packages is to only return data for probesets that
> target a single gene. This behavior is modifiable, however.
>
> What you have been getting is this:
>
>> get("1449880_s_at", mouse4302SYMBOL)
> [1] NA
>
> but we can allow multiple hits using toggleProbes():
>
>> x <- toggleProbes(mouse4302SYMBOL, "multiple")
>> get("1449880_s_at", x)
> [1] "Bglap"     "Bglap-rs1" "Bglap2"
>
> Best,
>
> Jim
>
>
>
>>
>> Thanks,
>> Andrew
>>
>> sessionInfo()
>>
>> R version 2.15.0 Patched (2012-03-30 r58877)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>> [1] C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] mouse4302.db_2.7.1   org.Mm.eg.db_2.7.1   RSQLite_0.11.1
>> DBI_0.2-5
>> [5] AnnotationDbi_1.18.0 Biobase_2.16.0       BiocGenerics_0.2.0
>> BiocInstaller_1.4.3
>>
>> loaded via a namespace (and not attached):
>> [1] IRanges_1.14.2 stats4_2.15.0  tools_2.15.0
>>
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>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>