[BioC] Gene Ontology analysis for non-affy data

[Marc Carlson]

Hi Yupu,

Lets keep this message on list so that others can benefit from our
discussion.  The annotation parameter is where you need to specify the
annotation package that you are going to use.  You can install the
appropriate annotation package using biocLite().  Most major platforms
are supported and the annotation package is traditionally named after
the platform that it is based on.  You can peruse our list of "stock"
annotation packages here:

http://www.bioconductor.org/packages/release/data/annotation/

Please let us know if the platform you are looking for is not there.  In
that case, we have also provided a way for you to make your own.  You
can find details on that in the SQLForge vignette in the AnnotationDbi
package:

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


  Marc



Yupu Liang wrote:
> Marc:
>
> Hi, thanks for the response and I have read the docs but I got
> confused/lost at
>
>
> params <- new("GOHyperGParams", geneIds = selectedEntrezIds,
> + universeGeneIds = entrezUniverse, annotation = "hgu95av2.db",
> + ontology = "BP", pvalueCutoff = hgCutoff, conditional = FALSE,
> + testDirection = "over")
>
> I am not sure what I should use for the annotation parameter
>
> And from the class description of GOHyperGParams-class, it says
>
> annotation:A string giving the name of the annotation data package for
> the chip used to generate the data.
>
> Yupu
>
>
> On Sep 16, 2009, at 5:51 PM, Marc Carlson wrote:
>
>> Hi Yupu,
>>
>> You should read the tutorial vignette for the GOstats package.  I think
>> it will probably show you what you need to know:
>>
>> You can find the GOstats package here:
>>
>> http://www.bioconductor.org/packages/release/bioc/html/GOstats.html
>>
>> And the tutorial here:
>>
>> http://www.bioconductor.org/packages/release/bioc/vignettes/GOstats/inst/doc/GOstatsHyperG.pdf
>>
>>
>>
>>
>>  Marc
>>
>>
>>
>>
>>
>> Yupu Liang wrote:
>>> Hi,
>>>
>>> I am new to GO analysis.
>>>
>>> What I want to do is pretty simple: I have a list of mouse gene (gene
>>> symbol as ID) from illumina expression experiment and I want to found
>>> out if any GO term is significantly enriched among these genes.
>>>
>>> It seems GOstats and topGO are all designed for Affymetrix data.
>>>
>>> I guess I could (in theory) use GO.db to query GO,but I am afraid of
>>> reinventing things.
>>>
>>> Any suggestions?
>>>
>>> Thanks!
>>> Yupu
>>>
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>>
>
>