Hi Rae,

It occurs to me that you might be referring to////
<http://www.chlamy.org/> Chlamydomonas, in which case you will be using
an unsupported organism.  We have some support for those however if you
look at the vignette in the file "GOstatsForUnsupportedOrganisms.pdf" in
the GOstats package:

http://www.bioconductor.org/packages/release/bioc/html/GOstats.html

You will have to find or generate a mapping between the genes for your
organism and the GO terms though.  You might want to check the blast2GO
project for that.


  Marc




On 06/25/2010 02:06 PM, Xiaohui Wu wrote:
> Hi all,
>
> There are some GO databases 'org.Hs.eg.db' available in Biocondutor, which can be used in some R packages like goProfiles. But I need to analyse the GO terms in Chlamy, and no corresponding GO db can be found. 
>
> Is there any document describing how to make GO db, I googled, but none was found. Or, is there any other way like using perl to relate the GO terms and genes and do some hypothesis tests between two groups of genes?
>
> Thanking you,
>
> Rae
>
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