[BioC] How to get ENTREZID from Gene symbol in bioconductor

[Srinivas Iyyer]

Dear Marc, 
thanks for the tip. 

I obtained gene symboles from hgug133plus2SYMBOL env
(from probesets if u133plus2). 

I do not have have data matrix for these genes. I just
have only list of gene symbols. 


Is there a way to juggle between SYMBOL <-> PROBEsetID
<-> SYMBOL/ENTREZID/....and rest of all
functionalities. 

> xx = mget(msba, revmap(org.Hs.egSYMBOL))
Error in .checkKeys(value, Rkeys(x), x at ifnotfound) :
invalid key "KNTC2"

I get the error with org.Hs.egSYMBOL.

Thanks
Srini




--- Marc Carlson <mcarlson at fhcrc.org> wrote:

> Srinivas Iyyer wrote:
> > Dear group: 
> > I have a vector of gene symbols. 
> > I want to get EntrezID for those gene symbols. 
> > I want to use hgu133plus2 as my annotation
> > environment. 
> >
> > how can I do it. 
> >
> > here is my vector:
> >
> > msba <- c('AURKA','CCNB2','TRIP13','EZH2','TYMS')
> >
> > when I have probesetid it is straightforward for
> me. 
> >
> > thanks for your help. 
> >
> > srini
> >
> >
> >
> >
> >      
>
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> >   
> 
> #I would use this library to save a couple steps:
> 
> library(org.Hs.eg.db)
> 
> #then you can choose one of two options:
> #use this if you are confident that your gene
> symbols are mainstream:
> mget(msba, revmap(org.Hs.egSYMBOL))
> 
> #OR if you want to be more inclusive about your
> symbols you can also use
> this:
> mget(msba, org.Hs.egALIAS2EG)
> 
> 
> #I see that in your case the 1st option is really
> better since you find
> everything with that already.
> 
> # Marc
>