Re: [R] [BioC] oligo ids

From: Eleni Christodoulou <elenichri_at_gmail.com>
Date: Mon, 19 May 2008 19:14:26 +0300

Thanks Sean!

Your reply was very helpful. I already got almost what I wanted. I have some NA values but I will look if I can find them through bibliography or an external tool.

Best Regards,
Eleni

On Mon, May 19, 2008 at 6:07 PM, Sean Davis <sdavis2_at_mail.nih.gov> wrote:

> On Mon, May 19, 2008 at 10:47 AM, Eleni Christodoulou
> <elenichri_at_gmail.com> wrote:
> > Dear list,
> >
> > I am having a set of human oligo ids (H200006022 H200002025 H300004703
> > H200000442 H200005719 H300018350) which I want to map to Ensembl or
> RefSeq.
> > I am sure R has a function to do that. I downloaded the {oligo} package
> and
> > tried to use the probeNames function. Although the factor of ologo ids is
> an
> > object (as the argument to probeNames should be) I retrieve the following
> > error:
> > probeNames(significant_genes[,1])
> > Error in function (classes, fdef, mtable) :
> > unable to find an inherited method for function "probeNames", for
> > signature "factor"
> >
> > where significant_genes is the factor with the oligo ids. Could anyone
> help
> > me with the format I should use in order to apply probeNames? Or if
> someone
> > has any other function in mind which can do the mapping I would be really
> > grateful to hear that.
>
> Hi, Eleni. The probeNames() function is not applicable here,
> unfortunately. You are asking a question related to annotating your
> array. Therefore, you need an annotation package. I think the IDs
> that you specified are Qiagen (Operon) IDs, so the place to look is in
> the annotation package associated with the Qiagen arrays:
>
> Assuming that you are using R 2.7.0 (you are, correct?), then you can do:
>
> source('http://bioconductor.org/biocLite.R')
> biocLite('hguqiagenv3.db')
> library(hguqiagenv3.db)
> mget(c('H200006022','H200002025'),hguqiagenenv3REFSEQ)
>
> The last command will return a list of mappings between those two
> oligo ids and RefSeq. Typing:
>
> hguqiagenv3()
>
> will tell you the other annotation sources available for your qiagen
> chip. Ensembl mappings are available, as are a bunch of other
> mappings.
>
> Let us know if you have more questions.
>
> Sean
>

        [[alternative HTML version deleted]]



R-help_at_r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Mon 19 May 2008 - 17:19:18 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Mon 19 May 2008 - 18:30:41 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.

list of date sections of archive