[BioC] How to get ENTREZID from Gene symbol in bioconductor
srini_iyyer_bio at yahoo.com
Wed Mar 12 23:11:22 CET 2008
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
> 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.
--- 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
> > thanks for your help.
> > srini
> > Be a better friend, newshound, and
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> #I would use this library to save a couple steps:
> #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
> 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
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