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 > > [[alternative HTML version deleted]]