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

[James W. MacDonald]

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