[BioC] illumina Infinium HumanMethylation27 detection-p-value

[Pan Du]

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