[BioC] oligo ids

[Sean Davis]

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