[BioC] Analysing DNA methylation microarrays in Bioconductor

Claus-Jürgen Scholz scholz at klin-biochem.uni-wuerzburg.de
Thu Jul 22 09:01:16 CEST 2010


Hi Paul,

take a look whether the packages rMAT, BAC and iChip fit your needs.
Also, packages Ringo and Starr provide functionality for ChIP-on-chip
(or MeDIP in your case) analysis, but more focussed on Nimblegen and
Affymetrix arrays, respectively.

Bests,
Claus-Jürgen


Am 21.07.2010 19:04, schrieb 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
>
>
>



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