Question

Illumina MethylationEPIC vs. 450K

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Ahdee ▴ 50

@ahdee-8938

Last seen 5 days ago

United States

Hi, has anyone worked with data from the new Illumina Epic dataset? It has over 850K vs 450K. I tried using methyAnalysis but getting errors because there does not seem to be any annotation packages like the IlluminaHumanMethylation450k.db.

This is my first time doing methylation analysis; so I'm stuck. Does anyone know what other packages/technique I can use to get around this annotation problem? I do not have the IDAT files but outputs from genomestudio as provided by our vendor. I could possibly get the IDAT files though if it helps.

Thank you in advance.

Ahdee

methylumi minfi illuminahumanmethylation450k.db 450k methyanalysis • 4.9k views

ADD COMMENT • link updated 8.8 years ago by Peter Hickey ▴ 740 • written 8.8 years ago by Ahdee ▴ 50

score 1 · Answer 1 · 2016-02-25

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Peter Hickey ▴ 740

@petehaitch

Last seen 4 weeks ago

WEHI, Melbourne, Australia

Hi Ahdee,

An annotation package for the MethylationEPIC array will be available in the next Bioconductor release (scheduled for April 15). In the meantime, you can test out the current version that is available from https://bitbucket.org/khansen/illumina_epic.

ADD COMMENT • link 8.8 years ago Peter Hickey ▴ 740

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Peter, this is awesome. Stupid question but I see two files, one is a manifest file? Do I just download and install this as usual with install.packages function? Thanks.

ADD REPLY • link 8.8 years ago Ahdee ▴ 50

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Would I also be able to use this with other packages like lumi: for example lumiMethyR requires an annotation IlluminaHumanMethylation450k.db, can I do something like, lumiMethyR("input.txt",lib="IlluminaHumanMethylationEPICanno.ilmn10.hg19") instead? thanks.

ADD REPLY • link 8.8 years ago Ahdee ▴ 50

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Link got moved to https://bitbucket.org/hansenlab/illumina_epic On Thu, Feb 25, 2016 at 9:01 PM, Kasper Daniel Hansen < kasperdanielhansen@gmail.com> wrote: > There are two packages on that webpage. Install them as you install any > other source tarball (I do R CMD INSTALL from the command line). > > Kasper > > On Thu, Feb 25, 2016 at 7:33 PM, Ahdee [bioc] <noreply@bioconductor.org> > wrote: > >> Activity on a post you are following on support.bioconductor.org >> >> User Ahdee <https: support.bioconductor.org="" u="" 8938=""/> wrote Comment: >> Illumina MethylationEPIC vs. 450K >> <https: support.bioconductor.org="" p="" 78873="" #78884="">: >> >> Peter, this is awesome. Stupid question but I see two files, one is a >> manifest file? Do I just download and install this as usual >> with install.packages function? Thanks. >> >> ------------------------------ >> >> Post tags: methylumi, minfi, illuminahumanmethylation450k.db, 450k, >> methyanalysis >> >> You may reply via email or visit >> C: Illumina MethylationEPIC vs. 450K >> > >

ADD REPLY • link 8.8 years ago Kasper Daniel Hansen ★ 6.5k

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There are two packages on that webpage. Install them as you install any other source tarball (I do R CMD INSTALL from the command line). Kasper On Thu, Feb 25, 2016 at 7:33 PM, Ahdee [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Ahdee <https: support.bioconductor.org="" u="" 8938=""/> wrote Comment: > Illumina MethylationEPIC vs. 450K > <https: support.bioconductor.org="" p="" 78873="" #78884="">: > > Peter, this is awesome. Stupid question but I see two files, one is a > manifest file? Do I just download and install this as usual > with install.packages function? Thanks. > > ------------------------------ > > Post tags: methylumi, minfi, illuminahumanmethylation450k.db, 450k, > methyanalysis > > You may reply via email or visit > C: Illumina MethylationEPIC vs. 450K >

ADD REPLY • link 8.8 years ago Kasper Daniel Hansen ★ 6.5k

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I don't know off hand whether it works out-of-the-box with lumi. Perhaps give it a try and report back with how you go.

ADD REPLY • link 8.8 years ago Peter Hickey ▴ 740

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I followed your posts and tried to load it in lumi, and got the error:

rawdata <- lumiMethyR("MethylationProfile.txt",lib="IlluminaHumanMethylationEPICanno.ilm10b2.hg19")

Error in match(x, table, nomatch = 0L) : object 'allAnnotation' not found

I am extremely new to the analysis. Any idea? Thank you.

ADD REPLY • link 8.6 years ago ryan.zhu99 • 0

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~~double post~~

ADD REPLY • link 8.8 years ago Peter Hickey ▴ 740