[BioC] GO over representation analysis

[Sean Davis]

On Fri, Aug 29, 2008 at 8:33 AM, michael watson (IAH-C)
<michael.watson at bbsrc.ac.uk> wrote:
> Dear All
>
> I think one thing that is frustrating here is that there is not a simple
> guide here for people who want to create an annotation package for an
> array that does not yet have one.
>
> Do we use AnnotationDbi?  Or AnnBuilder?  Or is there another way?
>
> What is the "best practice" for building an annotation package?

Hi, Mick.  The confusion arises because annotation packages have been
migrated from the environment-based packages built by AnnBuilder to
the newer SQLite-based packages of AnnotationDbi.  The answer depends
on which version of R and, therefore, which version of Bioconductor
you are using.  That said, the standard for the current and future
releases (for the near-future, anyway) is to use SQLForge from
AnnotationDbi.

Sean

> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Marc
> Carlson
> Sent: 25 August 2008 17:03
> To: Heike Pospisil
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] GO over representation analysis
>
> You could just make an annotation package for the array in question by
> using the SQLForge code in the AnotationDbi package.
> You can find instructions on how to do this here:
>
> http://www.bioconductor.org/packages/2.3/bioc/html/AnnotationDbi.html
>
> Let me know if you have any questions about SQLForge.
>
>
>  Marc
>
>
>
> Heike Pospisil wrote:
>> Hello Bioconductors,
>>
>> I am looking for a method to perfom over representation analysis (Gene
>
>> Ontology) within R. I have data from the Maize Oligonucleotide Array
> (two
>> channel) with the GO categories for all probes on this array. I have
>> clustered the genes using Maanova and I am interested in GO over
>> representation of the gene lists from these clusters.
>>
>> I know the GO tools from Bioconductor (e.g. GOstats), but I do not
> know how to
>> adapt the analysis to an 'unusual' array with no annotation data
> package and
>> now Entrez IDs. Any hints?
>>
>> Thanks in advance,
>> Heike
>>
>
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