[BioC] Agilent - GO

[Marc Noguera]

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

Thanks in advance

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