[BioC] Analysing DNA methylation microarrays in Bioconductor

[Paul Geeleher]

Hello List,

I've inherited microarray data from a bunch of Agilent CpG island
methylation arrays, 5 control and 5 disease samples. Basically the
arrays are set up as follows:

Cy3 - Methylated DNA from a patient's bowel isolated using IP.
Cy5 - DNA (Both methylated and unmethylated) from the bowel of the
same person as above.

Basically I'd like to identify regions of the genome (the individual
reporters or even better the CpG islands [I think there averages about
8 reporters per CpG island]) that are differentially methylated
between the 5 disease and 5 control samples.

So I'm wondering what packages (if any) in Bioconductor I could be
looking at to do this? I'd also welcome the suggestion of any other
software that might be out there?

Thanks,

Paul


-- 
Paul Geeleher
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland
Galway
Ireland
--
www.bioinformaticstutorials.com