[BioC] Dye bias adjustment of Illumina Infinium Methylation data
Shi, Tao
shidaxia at yahoo.com
Wed Sep 8 18:22:28 CEST 2010
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
> >>>
> >>> _______________________________________________
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> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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> >>> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>>
> >>
> >> [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
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> >
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> >
> >
> >
> >
>
>
> --
> 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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