illumina Infinium HumanMethylation27 detection-p-value
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Shi, Tao ▴ 720
@shi-tao-199
Last seen 7.1 years ago
Hi list, Does anybody know how the Illumina Infinium HumanMethylation27 detection-p-values are calculated? Thanks! ...Tao [[alternative HTML version deleted]]
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Pan Du ★ 1.2k
@pan-du-2010
Last seen 7.9 years ago
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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Hi Pan, Thank you! But do you have the exact formulas? ...Tao ________________________________ From: Pan Du <dupan@northwestern.edu> Cc: bioconductor@stat.math.ethz.ch Sent: Wed, August 25, 2010 7:57:25 AM Subject: Re: [BioC] illumina Infinium HumanMethylation27 detection-p-value 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) > 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 [[alternative HTML version deleted]]
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I guess they assume the Intensity distribution of negative control probes are Gaussian, then it is easy to calculate the p-value by providing the measured Intensity of the CpG site. But I have never tried. I would like to know the result if can verify this. Pan On 8/25/10 9:59 AM, "Shi, Tao" <shidaxia@yahoo.com> wrote: > Hi Pan, > > Thank you! But do you have the exact formulas? > > ...Tao > > > > From: Pan Du <dupan@northwestern.edu> > To: shidaxia@yahoo.com > Cc: bioconductor@stat.math.ethz.ch > Sent: Wed, August 25, 2010 7:57:25 AM > Subject: Re: [BioC] illumina Infinium HumanMethylation27 detection-p-value > > 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 > > > > > [[alternative HTML version deleted]]
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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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >>
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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 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> > > > > > >
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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 > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@stat.math.ethz.ch > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- 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) [[alternative HTML version deleted]]
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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 >>>> >> [[alternative HTML version deleted]]
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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) [[alternative HTML version deleted]]
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