[R] how to map microarray probe to gene, homology

[Ekta Jain]

Hi,
You could use the s apply function to create a data frame of the annotation. If hgu133 plus 2.0 is your chip something like the following could be employed

>myAnnot <- data.frame(ACCNUM=sapply(contents(hgu133plus2ACCNUM), paste, collapse=", "), SYMBOL=sapply(contents(hgu133plus2SYMBOL), paste, collapse=", "), +DESC=sapply(contents(hgu133plus2GENENAME), paste, collapse=", "));

or 
>ID <- featureNames(eset)
>Symbol <- getSYMBOL(ID, "hgu133plus2.db")
>tmp <- data.frame(ID=ID, Symbol=Symbol, Name=Name, Ensembl=Ensembl, stringsAsFactors=F)
>tmp[tmp=="NA"] <- NA # The stringsAsFactors makes "NA" characters
>fData(eset.norm) <- tmp

Regards,
Ekta
-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Peter Langfelder
Sent: 03 April 2012 23:00
To: email mail
Cc: r-help at r-project.org
Subject: Re: [R] how to map microarray probe to gene, homology

On Tue, Apr 3, 2012 at 7:21 AM, email mail <email8889 at gmail.com> wrote:
> Hi:
>
> I have clustered microarray gene expression data and trying to map between
> microarray probe, gene, pathway, gene ontology, and homology for a set of
> (affy) microarray probes. Is there any package in R which facilitates this?
> I am looking at bioconductor, but till now could not find a solution. A
> link to some worked example would be appreciated.

Yes, Bioconductor has annotation packages for microarray chips plus
other packages for connecting gene identifiers to (for example) gene
ontologies.

For example, the package hgu133plus2.db contains annotations for the
U133 plus 2 chip and you can use to map affy probe IDs to gene
symbols, IDs, GO terms etc. Install the package, load it, then type

ls("package:hgu133plus2.db")

and look at the help files for each topic for more details and examples.

The array annotations are chip-specific so you need to choose the
right package for your chip.

Peter

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