[BioC] mouse4302.db and can't find gene symbol annotation
yee at post.harvard.edu
Tue Oct 23 18:06:06 CEST 2012
Thanks for the information, that's extremely helpful.
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
>> 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)
>  NA
> but we can allow multiple hits using toggleProbes():
>> x <- toggleProbes(mouse4302SYMBOL, "multiple")
>> get("1449880_s_at", x)
>  "Bglap" "Bglap-rs1" "Bglap2"
>> R version 2.15.0 Patched (2012-03-30 r58877)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>  C
>> attached base packages:
>>  stats graphics grDevices utils datasets methods base
>> other attached packages:
>>  mouse4302.db_2.7.1 org.Mm.eg.db_2.7.1 RSQLite_0.11.1
>>  AnnotationDbi_1.18.0 Biobase_2.16.0 BiocGenerics_0.2.0
>> loaded via a namespace (and not attached):
>>  IRanges_1.14.2 stats4_2.15.0 tools_2.15.0
>> Bioconductor mailing list
>> Bioconductor at r-project.org
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> James W. MacDonald, M.S.
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
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