[BioC] illumina Infinium HumanMethylation27 detection-p-value

[weiliang Qiu]

Dear Professor Du,
Thanks for the information! Looking forward to using these new functions!

Sincerely yours,

Weiliang


On Wed, Aug 25, 2010 at 12:50 PM, Pan Du <dupan at 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 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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>
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