[BioC] illumina Infinium HumanMethylation27 detection-p-value

[Pan Du]

Hi Weiliang

It will include functions in data transformation (Beta-value, M-value),
color-bias adjustment, normalization and some QC plots. The functions are
still under active testing. We will upload most of these functions by the
end of Sept. More updates will be added in the next few months.

BTW, we use methylumi package to input the data.

Thanks for your interest!


Pan


On 8/25/10 11:27 AM, "weiliang Qiu" <weiliang.qiu at gmail.com> wrote:

> Dear Professor Du,
> It is great that lumi packge will include functions of preprocessiong
> methylation data.
> What functions will be available? Are they in the development version
> now? Many thanks!
> 
> Sincerely yours,
> 
> Weiliang
> 
> 
> On Wed, Aug 25, 2010 at 10:57 AM, Pan Du <dupan at northwestern.edu> wrote:
>> Hi Tao
>> 
>> The detection-p-value of Illumina methylation is estimated by comparing the
>> measured CpG site Intensity (methylated probe intensity + unmethylated probe
>> intensity) with the Intensity distribution of negative control probes.
>> Because it is measuring the DNA, the majority of CpG sites have very good
>> detection p-values (as long as the probe design is good and there is no
>> mutations or SNPs in the probe detecting region, it should have good
>> p-value.).
>> 
>> BTW, the lumi package will include functions of preprocessing Illumina
>> Infinium HumanMethylation27 in the coming release of Bioc.
>> 
>> Have a nice day
>> 
>> 
>> Pan
>> 
>> 
>> On 8/25/10 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
>> <bioconductor-request at stat.math.ethz.ch> wrote:
>> 
>>> Date: Tue, 24 Aug 2010 10:37:24 -0700 (PDT)
>>> From: "Shi, Tao" <shidaxia at yahoo.com>
>>> To: bioconductor <bioconductor at stat.math.ethz.ch>
>>> Subject: [BioC] illumina Infinium HumanMethylation27 detection-p-value
>>> Message-ID: <191131.61751.qm at web30804.mail.mud.yahoo.com>
>>> Content-Type: text/plain
>>> 
>>> Hi list,
>>> 
>>> Does anybody know how the Illumina Infinium HumanMethylation27
>>> detection-p-values are calculated?
>>> 
>>> Thanks!
>>> 
>>> ...Tao
>> 
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