DNA-Methylation, CopyNumber Results
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Ina Hoeschele ▴ 620
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Can someone please clarify for me the need for dye bias adjustment for Illumina Infinium methylation data? Below is an 'explanation' from Illumina to justfy why no dye adjustment is needed: "" ----- Original Message ----- From: "Sean Davis" <sdavis2@mail.nih.gov> To: "Chao-Jen Wong" <cwon2 at="" fhcrc.org=""> Cc: bioconductor at stat.math.ethz.ch Sent: Thursday, June 17, 2010 5:10:29 PM Subject: Re: [BioC] DNA-Methylation, CopyNumber Results On Thu, Jun 17, 2010 at 4:43 PM, Chao-Jen Wong <cwon2 at="" fhcrc.org=""> wrote: > As for Illumina Infinium methylation data, you can use the methylumi > package to manipulate the data and perform quality control and > normalization. Subsequently use limma to do differential methylation > analysis. > > Just keep in mind that the data from the Illumina arrays are pretty non-normal, so some assumptions that come into play when using a parametric testing method may be in question. Sean > On 06/16/10 19:22, Noemi Andor wrote: > > Hi, > > > > I need to parse some raw Methylation data from Illumina (Infinium) and > some copy number results (CGH, high amount of data). I would be grateful for > any useful information like which bioconducter packages to use, alternative > tools, normalization. > > > > thank's in advance, > > > > Noemi > > > > _______________________________________________ > > 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 > > > > > -- > Chao-Jen Wong > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Avenue N., M1-B514 > PO Box 19024 > Seattle, WA 98109 > 206.667.4485 > cwon2 at fhcrc.org > > _______________________________________________ > 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 > [[alternative HTML version deleted]] _______________________________________________ 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
Normalization Cancer limma copynumber Normalization Cancer limma copynumber • 2.0k views
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Ina Hoeschele ▴ 620
@ina-hoeschele-2992
Last seen 3.3 years ago
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Can someone please clarify for me the need for dye bias adjustment for Illumina Infinium methylation data? Below is an 'explanation' from Illumina to justfy why no dye adjustment is needed: "We actually have two different bead types for each locus, where the 3' terminus corresponds to the methylated and unmethylated condition. A single base extension is performed and the base after the methylation site is what actually determines the signal (red or green) for the locus. Since the base proximal to the methylation site will always be the same whether the site is methylated or not, your overall signal will always be in one color for a given locus. This means that no color normalization is necessary. This is probably more easily explained by taking a look at cartoon in the attached Data Sheet." Secondly, will methylumi, lumi and beadarray be able to deal with the new Infinium 450K methylation data? Many thanks ... Ina ----- Original Message ----- From: "Sean Davis" <sdavis2@mail.nih.gov> To: "Chao-Jen Wong" <cwon2 at="" fhcrc.org=""> Cc: bioconductor at stat.math.ethz.ch Sent: Thursday, June 17, 2010 5:10:29 PM Subject: Re: [BioC] DNA-Methylation, CopyNumber Results On Thu, Jun 17, 2010 at 4:43 PM, Chao-Jen Wong <cwon2 at="" fhcrc.org=""> wrote: > As for Illumina Infinium methylation data, you can use the methylumi > package to manipulate the data and perform quality control and > normalization. Subsequently use limma to do differential methylation > analysis. > > Just keep in mind that the data from the Illumina arrays are pretty non-normal, so some assumptions that come into play when using a parametric testing method may be in question. Sean > On 06/16/10 19:22, Noemi Andor wrote: > > Hi, > > > > I need to parse some raw Methylation data from Illumina (Infinium) and > some copy number results (CGH, high amount of data). I would be grateful for > any useful information like which bioconducter packages to use, alternative > tools, normalization. > > > > thank's in advance, > > > > Noemi > > > > _______________________________________________ > > 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 > > > > > -- > Chao-Jen Wong > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Avenue N., M1-B514 > PO Box 19024 > Seattle, WA 98109 > 206.667.4485 > cwon2 at fhcrc.org > > _______________________________________________ > 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 > [[alternative HTML version deleted]] _______________________________________________ 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 Ina Based on our experience, dye bias does exist in most of our datasets, and the bias is usually consistent within the same batch. If all your data is in the same batch, then usually no color bias adjustment is necessary for Illumina Infinium methylation data. This is consistent with the Illumina explanation as you described. However, if your data includes several different batches, then dye bias adjustment is important if the dye bias is quite different across different batches. The lumi package will include some color bias adjustment functions by the end of this month (before the new release of Bioc). The lumi package will also include support of Infinium 450K arrays in the future. Pan On 9/7/10 11:59 AM, "Ina Hoeschele" <inah at="" vbi.vt.edu=""> wrote: > Can someone please clarify for me the need for dye bias adjustment for > Illumina Infinium methylation data? Below is an 'explanation' from Illumina to > justfy why no dye adjustment is needed: > "We actually have two different bead types for each locus, where the 3' > terminus corresponds to the methylated and unmethylated condition. A single > base extension is performed and the base after the methylation site is what > actually determines the signal (red or green) for the locus. Since the base > proximal to the methylation site will always be the same whether the site is > methylated or not, your overall signal will always be in one color for a given > locus. This means that no color normalization is necessary. This is probably > more easily explained by taking a look at cartoon in the attached Data Sheet." > > Secondly, will methylumi, lumi and beadarray be able to deal with the new > Infinium 450K methylation data? > > Many thanks ... Ina > > > ----- Original Message ----- > From: "Sean Davis" <sdavis2 at="" mail.nih.gov=""> > To: "Chao-Jen Wong" <cwon2 at="" fhcrc.org=""> > Cc: bioconductor at stat.math.ethz.ch > Sent: Thursday, June 17, 2010 5:10:29 PM > Subject: Re: [BioC] DNA-Methylation, CopyNumber Results > > On Thu, Jun 17, 2010 at 4:43 PM, Chao-Jen Wong <cwon2 at="" fhcrc.org=""> wrote: > >> As for Illumina Infinium methylation data, you can use the methylumi >> package to manipulate the data and perform quality control and >> normalization. Subsequently use limma to do differential methylation >> analysis. >> >> > Just keep in mind that the data from the Illumina arrays are pretty > non-normal, so some assumptions that come into play when using a parametric > testing method may be in question. > > Sean > > > >> On 06/16/10 19:22, Noemi Andor wrote: >>> Hi, >>> >>> I need to parse some raw Methylation data from Illumina (Infinium) and >> some copy number results (CGH, high amount of data). I would be grateful for >> any useful information like which bioconducter packages to use, alternative >> tools, normalization. >>> >>> thank's in advance, >>> >>> Noemi >>> >>> _______________________________________________ >>> 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 >>> >> >> >> -- >> Chao-Jen Wong >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Avenue N., M1-B514 >> PO Box 19024 >> Seattle, WA 98109 >> 206.667.4485 >> cwon2 at fhcrc.org >> >> _______________________________________________ >> 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 >> > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 Pan, Could you please clarify the "dye bias" you're referring to? If you're referring to the bias between the two channels, I think it's clear to me from Illumina's document and the recent review article from Peter Laird in Nature Review Genetics, that there is no need of adjustment, as the two channels in Infinium are not corresponding to the methylation states. The normalization method of adjusting median of the two channels as used in methylumi is inappropriate for Infinium data. Could you please elaborate more on the color bias adjustment functions implemented in lumi? I'm really curious to see. Thanks! ...Tao ________________________________ From: Pan Du <dupan@northwestern.edu> To: Ina Hoeschele <inah at="" vbi.vt.edu=""> Cc: Simon Lin <s-lin2 at="" northwestern.edu="">; Sean Davis <sdavis2 at="" mail.nih.gov="">; bioconductor at stat.math.ethz.ch Sent: Tue, September 7, 2010 10:17:14 AM Subject: Re: [BioC] Dye bias adjustment of Illumina Infinium Methylation data Hi Ina Based on our experience, dye bias does exist in most of our datasets, and the bias is usually consistent within the same batch. If all your data is in the same batch, then usually no color bias adjustment is necessary for Illumina Infinium methylation data. This is consistent with the Illumina explanation as you described. However, if your data includes several different batches, then dye bias adjustment is important if the dye bias is quite different across different batches. The lumi package will include some color bias adjustment functions by the end of this month (before the new release of Bioc). The lumi package will also include support of Infinium 450K arrays in the future. Pan On 9/7/10 11:59 AM, "Ina Hoeschele" <inah at="" vbi.vt.edu=""> wrote: > Can someone please clarify for me the need for dye bias adjustment for > Illumina Infinium methylation data? Below is an 'explanation' from Illumina to > justfy why no dye adjustment is needed: > "We actually have two different bead types for each locus, where the 3' > terminus corresponds to the methylated and unmethylated condition. A single > base extension is performed and the base after the methylation site is what > actually determines the signal (red or green) for the locus. Since the base > proximal to the methylation site will always be the same whether the site is > methylated or not, your overall signal will always be in one color for a given > locus. This means that no color normalization is necessary. This is probably > more easily explained by taking a look at cartoon in the attached Data Sheet." > > Secondly, will methylumi, lumi and beadarray be able to deal with the new > Infinium 450K methylation data? > > Many thanks ... Ina > > > ----- Original Message ----- > From: "Sean Davis" <sdavis2 at="" mail.nih.gov=""> > To: "Chao-Jen Wong" <cwon2 at="" fhcrc.org=""> > Cc: bioconductor at stat.math.ethz.ch > Sent: Thursday, June 17, 2010 5:10:29 PM > Subject: Re: [BioC] DNA-Methylation, CopyNumber Results > > On Thu, Jun 17, 2010 at 4:43 PM, Chao-Jen Wong <cwon2 at="" fhcrc.org=""> wrote: > >> As for Illumina Infinium methylation data, you can use the methylumi >> package to manipulate the data and perform quality control and >> normalization. Subsequently use limma to do differential methylation >> analysis. >> >> > Just keep in mind that the data from the Illumina arrays are pretty > non-normal, so some assumptions that come into play when using a parametric > testing method may be in question. > > Sean > > > >> On 06/16/10 19:22, Noemi Andor wrote: >>> Hi, >>> >>> I need to parse some raw Methylation data from Illumina (Infinium) and >> some copy number results (CGH, high amount of data). I would be grateful for >> any useful information like which bioconducter packages to use, alternative >> tools, normalization. >>> >>> thank's in advance, >>> >>> Noemi >>> >>> _______________________________________________ >>> 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 >>> >> >> >> -- >> Chao-Jen Wong >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Avenue N., M1-B514 >> PO Box 19024 >> Seattle, WA 98109 >> 206.667.4485 >> cwon2 at fhcrc.org >> >> _______________________________________________ >> 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 >> > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 _______________________________________________ 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 Tao The dye bias in the same batch is not a big problem?but dye bias may cause severe batch effects. I will provide some example data in the lumi package to show the effects of dye bias when combining data in different batches. The basic idea of color bias adjustment is to normalize two color channels each other. You will see more details after I upload the functions to Bioc. The color bias functions may still need improvements. So your feedbacks are welcome. Pan On 9/7/10 7:10 PM, "Shi, Tao" <shidaxia at="" yahoo.com=""> wrote: > Hi Pan, > > Could you please clarify the "dye bias" you're referring to? If you're > referring to the bias between the two channels, I think it's clear to me from > Illumina's document and the recent review article from Peter Laird in Nature > Review Genetics, that there is no need of adjustment, as the two channels in > Infinium are not corresponding to the methylation states. The normalization > method of adjusting median of the two channels as used in methylumi is > inappropriate for Infinium data. > > Could you please elaborate more on the color bias adjustment functions > implemented in > > lumi? I'm really curious to see. > > Thanks! > > ...Tao > > > > > > > ________________________________ > From: Pan Du <dupan at="" northwestern.edu=""> > To: Ina Hoeschele <inah at="" vbi.vt.edu=""> > Cc: Simon Lin <s-lin2 at="" northwestern.edu="">; Sean Davis <sdavis2 at="" mail.nih.gov="">; > bioconductor at stat.math.ethz.ch > Sent: Tue, September 7, 2010 10:17:14 AM > Subject: Re: [BioC] Dye bias adjustment of Illumina Infinium Methylation data > > Hi Ina > > Based on our experience, dye bias does exist in most of our datasets, and > the bias is usually consistent within the same batch. If all your data is in > the same batch, then usually no color bias adjustment is necessary for > Illumina Infinium methylation data. This is consistent with the Illumina > explanation as you described. However, if your data includes several > different batches, then dye bias adjustment is important if the dye bias is > quite different across different batches. > > The lumi package will include some color bias adjustment functions by the > end of this month (before the new release of Bioc). The lumi package will > also include support of Infinium 450K arrays in the future. > > > Pan > > > On 9/7/10 11:59 AM, "Ina Hoeschele" <inah at="" vbi.vt.edu=""> wrote: > >> Can someone please clarify for me the need for dye bias adjustment for >> Illumina Infinium methylation data? Below is an 'explanation' from Illumina >> to >> justfy why no dye adjustment is needed: >> "We actually have two different bead types for each locus, where the 3' >> terminus corresponds to the methylated and unmethylated condition. A single >> base extension is performed and the base after the methylation site is what >> actually determines the signal (red or green) for the locus. Since the base >> proximal to the methylation site will always be the same whether the site is >> methylated or not, your overall signal will always be in one color for a >> given >> locus. This means that no color normalization is necessary. This is >> probably >> more easily explained by taking a look at cartoon in the attached Data >> Sheet." >> >> Secondly, will methylumi, lumi and beadarray be able to deal with the new >> Infinium 450K methylation data? >> >> Many thanks ... Ina >> >> >> ----- Original Message ----- >> From: "Sean Davis" <sdavis2 at="" mail.nih.gov=""> >> To: "Chao-Jen Wong" <cwon2 at="" fhcrc.org=""> >> Cc: bioconductor at stat.math.ethz.ch >> Sent: Thursday, June 17, 2010 5:10:29 PM >> Subject: Re: [BioC] DNA-Methylation, CopyNumber Results >> >> On Thu, Jun 17, 2010 at 4:43 PM, Chao-Jen Wong <cwon2 at="" fhcrc.org=""> wrote: >> >>> As for Illumina Infinium methylation data, you can use the methylumi >>> package to manipulate the data and perform quality control and >>> normalization. Subsequently use limma to do differential methylation >>> analysis. >>> >>> >> Just keep in mind that the data from the Illumina arrays are pretty >> non-normal, so some assumptions that come into play when using a parametric >> testing method may be in question. >> >> Sean >> >> >> >>> On 06/16/10 19:22, Noemi Andor wrote: >>>> Hi, >>>> >>>> I need to parse some raw Methylation data from Illumina (Infinium) and >>> some copy number results (CGH, high amount of data). I would be grateful for >>> any useful information like which bioconducter packages to use, alternative >>> tools, normalization. >>>> >>>> thank's in advance, >>>> >>>> Noemi >>>> >>>> _______________________________________________ >>>> 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 >>>> >>> >>> >>> -- >>> Chao-Jen Wong >>> Program in Computational Biology >>> Division of Public Health Sciences >>> Fred Hutchinson Cancer Research Center >>> 1100 Fairview Avenue N., M1-B514 >>> PO Box 19024 >>> Seattle, WA 98109 >>> 206.667.4485 >>> cwon2 at fhcrc.org >>> >>> _______________________________________________ >>> 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 >>> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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 > > > > -- Pan Du, PhD Research Assistant Professor Northwestern University Biomedical Informatics Center 750 N. Lake Shore Drive, 11-176 Chicago, IL 60611 Office (312) 503-2360; Fax: (312) 503-5388 dupan (at) northwestern.edu
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Thanks, Pan! Looking forward to your new functions! When they'll become available? ...Tao ----- Original Message ---- > From: Pan Du <dupan at="" northwestern.edu=""> > To: "Shi, Tao" <shidaxia at="" yahoo.com="">; Ina Hoeschele <inah at="" vbi.vt.edu=""> > Cc: Simon Lin <s-lin2 at="" northwestern.edu="">; Sean Davis <sdavis2 at="" mail.nih.gov="">; >bioconductor at stat.math.ethz.ch > Sent: Tue, September 7, 2010 6:34:54 PM > Subject: Re: [BioC] Dye bias adjustment of Illumina Infinium Methylation data > > Hi Tao > > The dye bias in the same batch is not a big problem?but dye bias may cause > severe batch effects. I will provide some example data in the lumi package > to show the effects of dye bias when combining data in different batches. > The basic idea of color bias adjustment is to normalize two color channels > each other. You will see more details after I upload the functions to Bioc. > The color bias functions may still need improvements. So your feedbacks are > welcome. > > > Pan > > > On 9/7/10 7:10 PM, "Shi, Tao" <shidaxia at="" yahoo.com=""> wrote: > > > Hi Pan, > > > > Could you please clarify the "dye bias" you're referring to? If you're > > referring to the bias between the two channels, I think it's clear to me >from > > Illumina's document and the recent review article from Peter Laird in Nature > > Review Genetics, that there is no need of adjustment, as the two channels in > > Infinium are not corresponding to the methylation states. The normalization > > method of adjusting median of the two channels as used in methylumi is > > inappropriate for Infinium data. > > > > Could you please elaborate more on the color bias adjustment functions > > implemented in > > > > lumi? I'm really curious to see. > > > > Thanks! > > > > ...Tao > > > > > > > > > > > > > > ________________________________ > > From: Pan Du <dupan at="" northwestern.edu=""> > > To: Ina Hoeschele <inah at="" vbi.vt.edu=""> > > Cc: Simon Lin <s-lin2 at="" northwestern.edu="">; Sean Davis <sdavis2 at="" mail.nih.gov="">; > > bioconductor at stat.math.ethz.ch > > Sent: Tue, September 7, 2010 10:17:14 AM > > Subject: Re: [BioC] Dye bias adjustment of Illumina Infinium Methylation >data > > > > Hi Ina > > > > Based on our experience, dye bias does exist in most of our datasets, and > > the bias is usually consistent within the same batch. If all your data is in > > the same batch, then usually no color bias adjustment is necessary for > > Illumina Infinium methylation data. This is consistent with the Illumina > > explanation as you described. However, if your data includes several > > different batches, then dye bias adjustment is important if the dye bias is > > quite different across different batches. > > > > The lumi package will include some color bias adjustment functions by the > > end of this month (before the new release of Bioc). The lumi package will > > also include support of Infinium 450K arrays in the future. > > > > > > Pan > > > > > > On 9/7/10 11:59 AM, "Ina Hoeschele" <inah at="" vbi.vt.edu=""> wrote: > > > >> Can someone please clarify for me the need for dye bias adjustment for > >> Illumina Infinium methylation data? Below is an 'explanation' from Illumina > >> to > >> justfy why no dye adjustment is needed: > >> "We actually have two different bead types for each locus, where the 3' > >> terminus corresponds to the methylated and unmethylated condition. A >single > >> base extension is performed and the base after the methylation site is what > >> actually determines the signal (red or green) for the locus. Since the >base > >> proximal to the methylation site will always be the same whether the site >is > >> methylated or not, your overall signal will always be in one color for a > >> given > >> locus. This means that no color normalization is necessary. This is > >> probably > >> more easily explained by taking a look at cartoon in the attached Data > >> Sheet." > >> > >> Secondly, will methylumi, lumi and beadarray be able to deal with the new > >> Infinium 450K methylation data? > >> > >> Many thanks ... Ina > >> > >> > >> ----- Original Message ----- > >> From: "Sean Davis" <sdavis2 at="" mail.nih.gov=""> > >> To: "Chao-Jen Wong" <cwon2 at="" fhcrc.org=""> > >> Cc: bioconductor at stat.math.ethz.ch > >> Sent: Thursday, June 17, 2010 5:10:29 PM > >> Subject: Re: [BioC] DNA-Methylation, CopyNumber Results > >> > >> On Thu, Jun 17, 2010 at 4:43 PM, Chao-Jen Wong <cwon2 at="" fhcrc.org=""> wrote: > >> > >>> As for Illumina Infinium methylation data, you can use the methylumi > >>> package to manipulate the data and perform quality control and > >>> normalization. Subsequently use limma to do differential methylation > >>> analysis. > >>> > >>> > >> Just keep in mind that the data from the Illumina arrays are pretty > >> non-normal, so some assumptions that come into play when using a parametric > >> testing method may be in question. > >> > >> Sean > >> > >> > >> > >>> On 06/16/10 19:22, Noemi Andor wrote: > >>>> Hi, > >>>> > >>>> I need to parse some raw Methylation data from Illumina (Infinium) and > >>> some copy number results (CGH, high amount of data). I would be grateful >for > >>> any useful information like which bioconducter packages to use, >alternative > >>> tools, normalization. > >>>> > >>>> thank's in advance, > >>>> > >>>> Noemi > >>>> > >>>> _______________________________________________ > >>>> 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 > >>>> > >>> > >>> > >>> -- > >>> Chao-Jen Wong > >>> Program in Computational Biology > >>> Division of Public Health Sciences > >>> Fred Hutchinson Cancer Research Center > >>> 1100 Fairview Avenue N., M1-B514 > >>> PO Box 19024 > >>> Seattle, WA 98109 > >>> 206.667.4485 > >>> cwon2 at fhcrc.org > >>> > >>> _______________________________________________ > >>> 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 > >>> > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> 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 > > > > _______________________________________________ > > 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 > > > > > > > > > > > -- > Pan Du, PhD > Research Assistant Professor > Northwestern University Biomedical Informatics Center > 750 N. Lake Shore Drive, 11-176 > Chicago, IL 60611 > Office (312) 503-2360; Fax: (312) 503-5388 > dupan (at) northwestern.edu > > > > > >
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On Tuesday 07 September 2010 19:17:14 Pan Du wrote: > Hi Ina > > Based on our experience, dye bias does exist in most of our datasets, and > the bias is usually consistent within the same batch. If all your data is > in the same batch, then usually no color bias adjustment is necessary for > Illumina Infinium methylation data. This is consistent with the Illumina > explanation as you described. However, if your data includes several > different batches, then dye bias adjustment is important if the dye bias is > quite different across different batches. We recently published a paper (Margaritis et al. 2009, Mol. Sys. Biol. 5:266; doi:10.1038/msb.2009.21) showing that 'local dye concentration' effects are responsible for dyebias in two-colour microarrays. If the sample is e.g. dUTP-labeled, both an increased A-content, increased melting temperature and an increased labeling percentage will increase the local dye concentration, and therefore increase the dye bias. The total dye bias therefore depends on both the hybridization and on the oligo-sequence. The Bioconductor package 'dyebias' contains code implementing the GASSCO method proposed in the paper, and really helps to reduce much of the dyebias. I don't know the details of the Illumina platform and protocols, but if the same premises apply, GASSCO should be able to address dyebias problems, also across different batches. I'd be interested to find out, so if you need help, feel free to contact me. Regards, Philip -- Philip Lijnzaad, PhD Holstege Genomics Laboratory Dept. of Molecular Cancer Research University Medical Center (UMC), Utrecht Stratenum room 3.137 (on Tuesdays and Thursdays not in after 15.00) MSN chat (*NOT* email): philip_lijnzaad at hotmail.com P.O. Box 85060, 3508 AB Utrecht (Universiteitsweg 100, 3584 CG Utrecht) The Netherlands tel: +31 (0)8875 68464 fax: +31 (0)8875 68479 ---------------------------------------------------------------------- -------- De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ---------------------------------------------------------------------- -------- This message may contain confidential information and is...{{dropped:8}}
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> I don't know the details of the Illumina platform and protocols, but if the > same premises apply, GASSCO should be able to address dyebias problems, also > across different batches. I'd be interested to find out, so if you need help, > feel free to contact me. Hi Philip, The Illumina Infinium platform is not the same as cDNA microarray. For a given methylation locus, methylated and unmethylated signals are always coming from the same channel, whereas in cDNA array, for each probe, the signals for sample and control are from two different channels. ...Tao > > Regards, > >Philip > > -- > Philip Lijnzaad, PhD > Holstege Genomics Laboratory > Dept. of Molecular Cancer Research > University Medical Center (UMC), Utrecht > Stratenum room 3.137 (on Tuesdays and Thursdays not in after 15.00) > MSN chat (*NOT* email): philip_lijnzaad at hotmail.com > P.O. Box 85060, 3508 AB Utrecht > (Universiteitsweg 100, 3584 CG Utrecht) > The Netherlands > tel: +31 (0)8875 68464 > fax: +31 (0)8875 68479 > > -------------------------------------------------------------------- ---------- > > De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is > uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht > ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct > te informeren door het bericht te retourneren. Het Universitair Medisch > Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de >W.H.W. > (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij > de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. > > Denk s.v.p aan het milieu voor u deze e-mail afdrukt. > > -------------------------------------------------------------------- ---------- > > This message may contain confidential information and is...{{dropped:8}} > > _______________________________________________ > 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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