[BioC] Analysing DNA methylation microarrays in Bioconductor

[Paul Geeleher]

Thanks for the replies guys,

Sean, we have 5 disease samples and 5 control samples. Each array has
244k reporters located in CpG islands, averaging about 8 reporters per
CpG island.

Jinyan, doesn't MEDME require some kind of calibration experiment?
Needless to say this hasn't been done and it's unlikely that there is
money there to do it.

Paul.

On Fri, Jul 23, 2010 at 7:02 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> Hi, Paul.  How many samples do you have?  And what are the sizes of the
> groups?
>
> It seems to me that you have for each probe a number.  You could do
> probewise testing between groups, or you could do some summarization first
> and then hypothesis testing.  In any case, there are a number of ways to
> arrive at an n x p matrix where standard statistical tools could be used.
>
> Sean
>
> On Jul 23, 2010 11:54 AM, "Paul Geeleher" <paulgeeleher at gmail.com> wrote:
>
> I understand your approach but the main problem I'd see with such a
> thresholding approach is that you are highly likely to find regions
> that are just below the cutoff to be called "methylated" in one
> phenotype and just above the threshold in the other phenotype. Thus
> most likely not differentially methylated at all. Do you see what I
> mean?
>
> Perhaps some kind of approach that labels each reporter as having a
> probability of methylation (and hence a probability of unmethylation),
> which can be compared across samples of a given phenotype to give a
> probability of all reporters being methylated/unmethylated in each
> phenotype, then compares these probabilities between phenotypes to
> give a probability of "differential methylation". That's just off the
> top of my head, I think it makes sense, but I'm presuming nothing like
> that has actually been implemented?
>
> Paul.
>
> On Fri, Jul 23, 2010 at 6:45 PM, Steve Lianoglou
> <mailinglist.honeypot at gmail.com> wrote:
>> Hi,
>>
>> ...
>
> --
> Paul Geeleher
> School of Mathematics, Statistics and Applied Mathematics
> National University of I...
>
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> Bioconductor at stat.math.ethz.ch
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-- 
Paul Geeleher
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland
Galway
Ireland
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www.bioinformaticstutorials.com