[BioC] Mapping Affy probes to OperonID or ensemblID

[Sean Davis]

On Nov 14, 2007 2:57 AM, Julian Lee <julian at omniarray.com> wrote:
> Hi all,
>
> I'm relatively new to R/Bioconductor.
>
> I'm trying to map Affy's HGU133plus2 probesids with OperonID/EnsemblIDs
>
> Eg.
> OperonIDs
> H200007039

These IDs are not really considered public identifiers.  They are
related to a particular microarray platform.

> EnsemblIDs
> ENSG00000169678

These IDs are public identifiers.

> Desc
> Linker for activation of T cells (36 kDa phospho-tyrosine adaptor protein) (pp36) (p36-38).
>
> DB website link
> http://omad.operon.com/human2/index.php
>
> Is there an environment for OperonIDs in the hgu133plus2 package?

No.

> Eg.
> library(hgu133plus2)
> xx<-as.list(hgu133plus2OPERONID)
> myU133plus2probes<-xx[match(operonidsofinterest,xx)]
>
> If there isn't, could we build one?

You could, yes.  However, Bioconductor probably will not, since Operon
IDs are not public identifiers.

I can only guess what your use case is, but I would suggest that you
look into using the biomaRt package to map hgu133plus2 IDs to Ensembl
gene ids.  If I recall, Operon was designed against Ensembl genes.
Then, you can use standard R functions like merge() and match() to map
the hgu133plus2 probes to Operon probes using the common Ensembl gene
ids.

Sean