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

[Yong Li]

Hi Wendy,

for something like this the function aggregate should do the job. type

?aggregate

in R for more details.

Yong Li

Wendy Qiao 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
>>>
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>>>
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>> --
>> 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
>> **********************************************************
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> 
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> 
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