Dear Marc,

Thanks for your prompt replied.

Your information is helpful. You are right about the organism I'm working
on. It is not a model species nor human samples, it is a gymnosperm plant
species.

I will have a look on the ?makeOrgPackageFromNCBI package from the manual,
hopefully I have luck on this. It is a bit pity that many nice GO packages
are not yet ready for non-model species, please correct me if I was wrong.

You did answered my question. Thanks for your time and advice. Have a nice
weekend.

Best regards,
KJ Lim



On 22 September 2012 03:49, Marc Carlson <mcarlson@fhcrc.org> wrote:

> Hi Lim,
>
> First of all it all depends on what you have for gene identifiers.  If you
> are like most people you will have entrez gene IDs.  So for now I will
> assume you have those.
>
> ## So lets further assume you are working with humans and just choose the
> 1st two entrez gene IDs so that we can make a (hopefully meaningful) example
> ids = c("1","2")
> ## now load the org library for humans
> library(org.Hs.eg.db)
> ## then you can call select to extract your GO IDs like this:
> select(org.Hs.eg.db, keys = ids, cols = "GO", keytype = "ENTREZID")
>
> Now one thing to notice is that if you have some other kind of identifier,
> then your keytype argument will have to be set to a different value.  And
> hopefully, the kind of ID you are using, is present in the package that you
> have to search...  See the manual page for select for more information.
>
> ?select
>
> From your question, I also recognize that you may not be able to do this
> because it sounds like you might be using a more unusual organism and not
> be using something commonplace like human.  Well don't give up just yet,
> because we may be able to help you there too.  You can look at the manual
> page for the function makeOrgPackageFromNCBI to learn how you can try to
> generate an org package from just the taxonomy ID (which you can look up on
> NCBIs website).  If the data is available at NCBI, then you should be able
> to generate a package from NCBI that will match your organism of choice.
>
> ?makeOrgPackageFromNCBI
>
>
> Does that answer your question?
>
>
>   Marc
>
>
>
>
> On 09/21/2012 02:35 AM, KJ Lim wrote:
>
>> Dear Bioconductor community,
>>
>> Good day.
>>
>> I did the differential expression analysis for my RNA-Seq data with edgeR
>> package. I have a list of differentially expressed genes now and I would
>> like to find the GO terms for the genes.
>>
>> I have been reading and searching around for the right package. But, I
>> found that several packages are developed based on model species. Could
>> the
>> community kindly please suggest me what GO annotation package I can use
>> for
>> non-model species; plant RNA-Seq data?
>>
>> Thank you very much and have a nice weekend.
>>
>> Best regards,
>> KJ Lim
>>
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>>
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