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@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
>>
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>>
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
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