[BioC] How to perform annotation using refseq IDs and GO ?

[Georg Otto]

Hi,

if your organism is in the Ensembl database, you can use the biomaRt
package to retrieve GO annotations. biomaRt is explained quite nicely
in

www.stat.berkeley.edu/~steffen/BioC2007-biomaRt.pdf


For example, if geneids.rm is a vector of RefSeq RNA ids, you can
retrieve the associated GO annotations like this:

getBM(attributes=c("go", "go_description"), filters="refseq_dna",
                          values= geneids.nm,
                          mart=ensembl)


To perform statistical analysis on GO terms, have a look at the
GOstats package.

Best,

Georg


"Ng Stanley" <stanleyngkl at gmail.com> writes:

>
> Given a list of refseq IDs obtained from a microarray, what packages and
> steps are needed to perform analysis using the Gene Ontology ?
>