Question: Differential expression on individual Affy probes (Peter Saffrey)
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9.7 years ago by
L L30
L L30 wrote:
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 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: 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 > Date: Fri, 9 Oct 2009 18:00:42 +0100 > From: "Peter Saffrey" <> > Subject: [BioC] Differential expression on individual Affy probes > To: <> > Message-ID: > <> > 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: > > > > 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]]
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