[BioC] How to include chromosomal location or GO-annotation data in supervised microarray analysis?

[Rainer Tischler]

Hi,

I have a microarray data set with additional information on the chromosomal location of genes and their GO-groups. I'm looking for a simple way to include this annotation data in a supervised microarray analysis (disease outcome classification) to improve the prediction accuracy. There appear to be two basic strategies:

1. combine similar genes to gene groups based on the annotation data before starting the statistical analysis
2. improve the distance measure for feature selection and classification by including distance information derived from the annotation data

Is anybody aware of an R-package that implements one of these ideas or is there a simply way I could implement this myself (e.g. replacing gene groups by a single gene based on the mean or median expression levels - I'm not sure whether this would be effective or whether more sophisticated methods are already available as R-packages)?
Currently, I'm using an SVM- and a PAM-classifier for my predictions, thus, I hope to find an integrative approach which is compatible with these classifiers.

Many thanks,
Rainer

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