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List:       bioconductor
Subject:    Re: [BioC] illumina Infinium HumanMethylation27 detection-p-value
From:       "Tim Triche, Jr." <ttriche () usc ! edu>
Date:       2010-08-28 1:14:12
Message-ID: AANLkTikZwrA8P_178LoWFuEYjWKD8rxCj_o6r=GjMN8m () mail ! gmail ! com
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Of course -- the probes with multiple perfect matches to the genome are not
very informative!

However, in some of the probes, multiple CpG sites are interrogated.  So I
was wondering whether you just aligned those and mapped them to NuIDs
corresponding to the remaining 47 or 48 bases in common.  It will get worse
on the 450k chips, after all.


On Fri, Aug 27, 2010 at 12:22 PM, Pan Du <dupan@northwestern.edu> wrote:

>  Hi Tim
>
> Like expression microarrays, the methylation probe are also supposed to be
> uniquely mapped to one corresponding CpG site. But multiple CpG sites might
> be measured for the promoter region of each gene. If one probe is mapped to
> multiple sites, it is a bad probe design and should be filtered away.
> As for NuID encoding of methylation probe sequences, so far we have not
> done that for Illumina methylation data yet. We just use Illumina ID as
> identifier and use IlluminaHumanMethylation27k.db annotation package.
>
>
> Pan
>
>
>
>
> On 8/27/10 12:57 PM, "Tim Triche" <tim.triche@gmail.com> wrote:
>
> How do you handle the NuID encoding for probes with multiple CpG sites?
>
> --t
>
>
>
> On Wed, Aug 25, 2010 at 9:50 AM, Pan Du <dupan@northwestern.edu> wrote:
>
> 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@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@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@stat.math.ethz.ch"
> >> <bioconductor-request@stat.math.ethz.ch> wrote:
> >>
> >>> Date: Tue, 24 Aug 2010 10:37:24 -0700 (PDT)
> >>> From: "Shi, Tao" <shidaxia@yahoo.com>
> >>> To: bioconductor <bioconductor@stat.math.ethz.ch>
> >>> Subject: [BioC] illumina Infinium HumanMethylation27 detection-p-value
> >>> Message-ID: <191131.61751.qm@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
> >>
>
>


-- 
The aim of science is to seek the simplest explanations of complex facts. We
are apt to fall into the error of thinking that the facts are simple because
simplicity is the goal of our quest... Seek simplicity, and distrust it.

Alfred North Whitehead, *The Concept of Nature* (1920)

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