[BioC] mouse4302.db and can't find gene symbol annotation
mcarlson at fhcrc.org
Tue Oct 23 19:37:44 CEST 2012
You can also just get your symbols this way:
select( mouse4302.db, keys ="1449880_s_at", cols="SYMBOL",
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.
On 10/23/2012 09:06 AM, Andrew Yee wrote:
> 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
>>> Search the archives:
>> James W. MacDonald, M.S.
>> University of Washington
>> Environmental and Occupational Health Sciences
>> 4225 Roosevelt Way NE, # 100
>> Seattle WA 98105-6099
More information about the Bioconductor