[BioC] Agilent - GO

Sean Davis seandavi at gmail.com
Tue Jan 12 14:02:12 CET 2010

On Tue, Jan 12, 2010 at 4:26 AM, Marc Noguera <mnoguera at imppc.org> wrote:
> Thanks for the help Sean, It has been very useful.
> I have managed to create the geneUniverse from chip data and run the
> hyperGTests on my selected genesets looking for enrichment.
> Now I have hyperGResults instances as a result, and apart from summary
> information on MF, BP or CC with the corresponding p-values I would like
> to know how could I run some kind of FDR corrections on these results.

The correct statistical treatment of nested categories is probably
still a topic of research.  However, our own Seth Falcon and Robert
Gentleman (among others) have looked into this:


> Also, what are the available tools for visualizing such data. I am
> checking topGO now, but maybe there are some other tools.

I'm not sure what you mean by "visualizing", but take a look at the
Rgraphviz package.


> Marc
> Sean Davis wrote:
>> On Mon, Jan 11, 2010 at 7:15 AM, Marc Noguera <mnoguera at imppc.org> wrote:
>>> Dear list,
>>> I am trying to find function enrichment for a gene list that we have
>>> obtained through chip-chip experiments. The chip that we have used is
>>> the Agilent human promoter array, which consists of two differents slides.
>>> I cannot find any package corresponding to the annotation of this chip,
>>> which I think I need to obtain "gene universe" information and, from
>>> there, obtain gene set enrichments using GO. Does an annotation package
>>> for that chip exists or should I build the annotation package myself,
>>> and if so, could you provide pointers to how to build it?
>> Hi, Marc.  The chip annotation packages will not be helpful for this
>> situation, as they are gene-based.  Your chips are not gene-based, so
>> an annotation package built for them, even if you could get it built,
>> probably wouldn't make a lot of sense.  Instead, you will probably
>> need to generate a gene list of all genes covered by the array and
>> then a gene list of the genes showing promoter signal.  With those two
>> lists, you should be able to define your universe and use the
>> org.Hs.eg.db package for GO enrichment.
>> Sean
> --
> -----------------------------------------------------
> Marc Noguera i Julian, PhD
> Genomics unit / Bioinformatics
> Institut de Medicina Preventiva i Personalitzada
> del Càncer (IMPPC)
> B-10 Office
> Carretera de Can Ruti
> Camí de les Escoles s/n
> 08916 Badalona, Barcelona
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