[BioC] Agilent - GO

[Sean Davis]

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