The detection-p-value of Illumina methylation is estimated by
measured CpG site Intensity (methylated probe intensity + unmethylated
intensity) with the Intensity distribution of negative control probes.
Because it is measuring the DNA, the majority of CpG sites have very
detection p-values (as long as the probe design is good and there is
mutations or SNPs in the probe detecting region, it should have good
BTW, the lumi package will include functions of preprocessing Illumina
Infinium HumanMethylation27 in the coming release of Bioc.
Have a nice day
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
> 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?