Hi Stanley,
Ng Stanley wrote:
> Hi,
>
> Given a list of refseq IDs obtained from a microarray, what packages
and
> steps are needed to perform analysis using the Gene Ontology ?
I am assuming here that you are not talking about an Affy array? If
you
are, the easiest thing to do would be to use GOstats and the
corresponding annotation package for that chip.
If we are not talking about an Affy chip, ideally one would still be
able to use GOstats and one of the org.Xx.eg.db packages, but I don't
know if any functionality for such an approach exists at this time.
You could also use topGO using one of the org.Xx.eg.db packages
(assuming that the species you are using is one of the six for which
an
org.Xx.eg.db package exists).
You might also consider a GSEA approach using the Category package.
As Georg Otto mentioned, you might also consider annotating your data
using biomaRt, but this approach will not work for GOstats. It will
work
for topGO, and might work for Category, although I am not 100% sure
about that one.
All of these packages have vignettes that you can read to help you get
started.
Best,
Jim
>
> If this question has been tackled before, will be grateful if
resource to
> the solution be pointed.
>
> Thanks
> Stanley
>
> [[alternative HTML version deleted]]
>
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--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
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 ?
>
