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

Georg Otto georg.otto at tuebingen.mpg.de
Thu Feb 28 11:06:20 CET 2008


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


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,

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



"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 ?

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