[BioC] Analysing DNA methylation microarrays in Bioconductor

[Paul Geeleher]

Interesting. I'm not sure it'd make sense to use expression values
(log ratios I assume) because while there might be a statistically
significant difference between the expression levels in each of the
phenotypes, that doesn't necessarily imply that the reporters are
methylated in one phenotype and unmethylated in the other if you see
what I mean?

I'm assuming in the second case you are refering to a p-value for to
the probability of methylation of each reporter. Maybe this makes more
sense, but I think you still need one phenotype to have high
probabilty of methylation and the other phenotype to have high
probability of unmethylation, along with a statistically significant
difference in the p-values between the phenotypes?

Paul.

On Fri, Jul 23, 2010 at 8:02 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
>
> On Fri, Jul 23, 2010 at 12:51 PM, Paul Geeleher <paulgeeleher at gmail.com>
> wrote:
>>
>> 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.
>>
>
> So, why not generate a 10 x 244k matrix or 10 x 30k matrix if you summarize
> over CpG island and then apply a hypothesis test of your choice (which might
> need to be nonparametric, even) to the data?  The value associated with each
> probe per sample could be either a raw value (after "appropriate
> normalization") or it could be derived from a number of ChIP-chip like
> analysis packages (ACME, tilingarray, etc.).
> Sean
>
>>
>> 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...
>> >
>> > Bioconductor mailing list
>> > Bioconductor at stat.math.ethz.ch
>> > https://stat.ethz.ch/mailman/listinfo/bioco...
>>
>>
>>
>> --
>> Paul Geeleher
>> School of Mathematics, Statistics and Applied Mathematics
>> National University of Ireland
>> Galway
>> Ireland
>> --
>> www.bioinformaticstutorials.com
>>
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>
>



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