Dear Peter,

"RPA" package implements a probabilistic method for probe-level differential
gene expression analysis on Affymetrix arrays, and is in review for the next
BioC release (see
http://www.bioconductor.org/packages/2.5/bioc/html/RPA.html). The package
also provides tools to analyze the reliability of individual probes.

"PECA" R package might be also useful for your purposes. This package
performs probe-level differential gene expression analysis for both ordinary
Affymetrix gene expression arrays and exon arrays (see the references on the
website). This package is currently not in BioConductor:
http://www.math.utu.fi/en/research/groups/bio/projects/peca.html

You can check the source code to find out how probe-level differential
expression is calculated in these packages. I hope this helps.

Leo Lahti,
Finland
http://www.cis.hut.fi/lmlahti


> Date: Fri, 9 Oct 2009 18:00:42 +0100
> From: "Peter Saffrey" <pzs@dcs.gla.ac.uk>
> Subject: [BioC] Differential expression on individual Affy probes
> To: <bioconductor@stat.math.ethz.ch>
> Message-ID:
>        <BED9D15F73EDDE48BF480604236A456005DCF50C@ex1.ad.dcs.gla.ac.uk>
> Content-Type: text/plain
>
>
> I have a set of Affy human gene expression arrays (HG-U133_Plus2.1) CEL
> files representing a treated sample over a number of time points. I'd like
> to compare the expression of these files not just on the genes they probe
> but on the exons.
>
> I know I should be using exon arrays for this, but what I have is a gene
> arrays, so I want to see how much I can do with that. If I can find the
> differential expression in an individual probe, I can map it to an exon.
> This should give me a limited view of which exons are changing expression
> between the arrays.
>
> I was planning to use the Rank Product method:
>
> http://www.bioconductor.org/packages/bioc/html/RankProd.html
>
> as the differential expression algorithm. Can anybody give me any advice on
> adapting this to work on individual probes, rather than whole genes? Or am I
> completely wasting my time on this?
>
> Peter
>
>

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