[BioC] package for collapsing probe id to entrezid or gene symbols

[Paul Geeleher]

This is one option:
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp

Paul.

On Tue, Mar 15, 2011 at 4:43 PM, Wendy Qiao <wendy2.qiao at gmail.com> wrote:
> Thank you, James.
>
> Sorry, I did not make my question clear.
>
> What I meant is that, on a chip, there are multiple probes for the same
> gene. I was wondering if there is a package or command that can combine the
> expression values on multiple probes for the same gene to one value by
> taking the median or average. It is not hard to write the code for doing
> this, but I was just wondering if there is existing package for doing this.
>
> Wendy
>
> On 15 March 2011 12:03, James W. MacDonald <jmacdon at med.umich.edu> wrote:
>
>> Hi Wendy,
>>
>>
>> On 3/15/2011 11:30 AM, Wendy Qiao wrote:
>>
>>> Hi all,
>>>
>>> I am searching for a Bioconductor package that can collapse affymetrix
>>> probe
>>> id to gene symbols or entrez id, but I have not had any luck yet. Does
>>> anyone know any package that can collapse the probe id to gene symbols?
>>>
>>
>> What exactly do you mean by 'collapse the probe id to gene symbol'? There
>> are annotation packages for pretty much all of the Affy chips that will map
>> probesets to either Entrez Gene ID or gene symbol (e.g., for the
>> HG-U133Plus2 chip we have the hgu133plus2.db package). These provide the
>> mappings in a simple way, using either get() or mget():
>>
>> > get("1007_s_at", hgu95av2ENTREZID)
>> [1] "780"
>> > get("1007_s_at", hgu95av2GENENAME)
>> [1] "discoidin domain receptor tyrosine kinase 1"
>> > get("1007_s_at", hgu95av2SYMBOL)
>> [1] "DDR1"
>>
>> But maybe you are looking for something else?
>>
>> Best,
>>
>> Jim
>>
>>
>>
>>> Thank you in advance,
>>> Wendy
>>>
>>>        [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>
>> --
>> James W. MacDonald, M.S.
>> Biostatistician
>> Douglas Lab
>> University of Michigan
>> Department of Human Genetics
>> 5912 Buhl
>> 1241 E. Catherine St.
>> Ann Arbor MI 48109-5618
>> 734-615-7826
>> **********************************************************
>> Electronic Mail is not secure, may not be read every day, and should not be
>> used for urgent or sensitive issues
>>
>
>        [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>



-- 
Paul Geeleher (PhD Student)
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland
Galway
Ireland
--
www.bioinformaticstutorials.com