[BioC] illumina Infinium HumanMethylation27 detection-p-value

Pan Du dupan at northwestern.edu
Wed Aug 25 16:57:25 CEST 2010

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

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 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

More information about the Bioconductor mailing list