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

[James W. MacDonald]

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]]
>
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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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