
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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