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

[Marc Carlson]

Hi Andrew,

You can also just get your symbols this way:

library(mouse4302.db)
library(org.Mm.eg.db)
select(  mouse4302.db, keys ="1449880_s_at", cols="SYMBOL", 
keytype="PROBEID")

This query will give you a warning because your probe will match to 
multiple symbols, but it avoids the step of having to create a special 
bimap that is set to expose all probes 1st.


   Marc


On 10/23/2012 09:06 AM, Andrew Yee wrote:
> 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
>>