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@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@gmail.com> wrote:
> Hi,
>
> ...

-- 
Paul Geeleher
School of Mathematics, Statistics and Applied Mathematics
National University of I...

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