Question: Illumina MethylationEPIC vs. 450K
1
gravatar for Ahdee
3.5 years ago by
Ahdee40
United States
Ahdee40 wrote:

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

 

ADD COMMENTlink modified 3.5 years ago by Peter Hickey450 • written 3.5 years ago by Ahdee40
Answer: Illumina MethylationEPIC vs. 450K
1
gravatar for Peter Hickey
3.5 years ago by
Peter Hickey450
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Peter Hickey450 wrote:

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 COMMENTlink written 3.5 years ago by Peter Hickey450

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 REPLYlink written 3.5 years ago by Ahdee40

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 REPLYlink modified 3.5 years ago • written 3.5 years ago by Ahdee40
2
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 REPLYlink written 3.5 years ago by Kasper Daniel Hansen6.4k
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 REPLYlink written 3.5 years ago by Kasper Daniel Hansen6.4k

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 REPLYlink modified 3.5 years ago • written 3.5 years ago by Peter Hickey450

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 REPLYlink written 3.3 years ago by ryan.zhu990

double post

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by Peter Hickey450
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 320 users visited in the last hour