[BioC] Analysing DNA methylation microarrays in Bioconductor

Paul Geeleher paulgeeleher at gmail.com
Fri Jul 23 19:35:20 CEST 2010


Thanks for your reply Claus,

What I've noticed however about these and every other tool I've found
is that they seem to be able to characterize a methlyation pattern in
a sample. I.e. say "this region appears to be methylated in this
sample".

What I'd like is something that can compare the methylation levels
between the samples, basically outputting a probability that a
region/reporter is methylated in one phenotype and unmethylated in the
other. It would be great if anyone could point me towards such a tool,
or confirm that it doesn't actually exist?

Thanks,

Paul

2010/7/22 Claus-Jürgen Scholz <scholz at klin-biochem.uni-wuerzburg.de>:
> 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
>>
>>
>>
>



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



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