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Question: support for EPIC methylation arrays in minfi
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gravatar for Kasper Daniel Hansen
20 months ago by
United States
Kasper Daniel Hansen6.3k wrote:

Illumina has released a new annotation file for the EPIC array, the new one is version 1.0b2.  Manifest and annotation packages have been updated, see
   https://bitbucket.org/hansenlab/illumina_epic
(Annotation packages are under review at Bioconductor).

Because of a name change in the annotation file, version 1.17.9 or better of minfi is required for full, easy support.  This version ought to propagate through the Bioconductor build system soon.  Read IDAT files using read.metharray.exp().

Best,
Kasper

ADD COMMENTlink modified 15 months ago by line.heylen0 • written 20 months ago by Kasper Daniel Hansen6.3k

Dear Kasper,

If I already have a list of CpGs with p-values etc, how do I merge this list to the EPIC annotation? For 450K data, I did this by using ChAMP and probe.features, but the EPIC probe.features object entails only chromosome and mapinfo, no information on gene, gene feature (like TSS; exon, intergenic) and CpG island. Is there a way to get this information? 

Thank you for your help.

Kind regards,

Line

 

ADD REPLYlink written 17 months ago by line.heylen0
probe.features is something ChAMP specific, so I can't help you there. You can get the full annotation object from EPIC by doing something like getAnnotation(XX) where XX might be you original RGset of Mset or whatever you have. Then you can merge based on CpG names. On Fri, Jun 3, 2016 at 9:39 AM, line.heylen [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User line.heylen <https: support.bioconductor.org="" u="" 10822=""/> wrote Comment: > support for EPIC methylation arrays in minfi > <https: support.bioconductor.org="" p="" 79876="" #83344="">: > > Dear Kasper, > > If I already have a list of CpGs with p-values etc, how do I merge this > list to the EPIC annotation? For 450K data, I did this by using ChAMP and > probe.features, but the EPIC probe.features object entails only chromosome > and mapinfo, no information on gene, gene feature (like TSS; exon, > intergenic) and CpG island. Is there a way to get this information? > > Thank you for your help. > > Kind regards, > > Line > > > > ------------------------------ > > Post tags: minfi > > You may reply via email or visit > C: support for EPIC methylation arrays in minfi >
ADD REPLYlink written 17 months ago by Kasper Daniel Hansen6.3k

Hi Kasper,

I downloaded the new EPIC annotation package at Bioconductor (biocLite("IlluminaHumanMethylationEPICanno.ilm10b2.hg19")) but do not know how to extract the annotation from this data to a dataframe consisting of a column of CpGs with columns like p-values and T statistic; and I getting strange errors since (such as: lazy-load database '/Library/Frameworks/R.framework/Versions/3.3/Resources/library/minfi/help/minfi.rdb' is corrupt). 

Thank you for your help.

 

Best,

Line

ADD REPLYlink written 15 months ago by line.heylen0

Dear Kasper,

I'm trying to merge the data of 3 datasets of individuals, all of them analyzed by Illumina Methylation EPIC arrays (i.e: arrayEPIC1, arrayEPIC2, arrayEPIC3). I've done the normalization of each array separately, I've filtered them by many available package filters and then I've converted each into 3 Methylsets. I want to analyze all individuals (different in the 3 arrays) from the arrays together so I have to merge the 3 Methylsets by the rownames (features) present in all Methylsets. I'm trying to do it with the combine() or combineArrays() function but there are some probes that are not present in all Methylsets so the number of features differs between datasets and an error message appears. In addition, I've different individuals in each Methylset (non conforming colnames) so I want to merge all individuals by the post filtering coincident probes. 

I would be very grateful if you can help me with this issue.

Thanks in advance!

Kind regards,

Paula

ADD REPLYlink written 9 months ago by paularl37730
Could you copy and paste code + error. Best, Kasper (Sent from my phone.) > On Feb 22, 2017, at 12:05, paularl3773 [bioc] <noreply@bioconductor.org> wrote: > > Activity on a post you are following on support.bioconductor.org > User paularl3773 wrote Comment: support for EPIC methylation arrays in minfi: > > Dear Kasper, > > I'm trying to merge the data of 3 datasets of individuals, all of them analyzed by Illumina Methylation EPIC arrays (i.e: arrayEPIC1, arrayEPIC2, arrayEPIC3). I've done the normalization of each array separately, I've filtered them by many available package filters and then I've converted each into 3 Methylsets. I want to analyze all individuals (different in the 3 arrays) from the arrays together so I have to merge the 3 Methylsets by the rownames (features) present in all Methylsets. I'm trying to do it with the combine() or combineArrays() function but there are some probes that are not present in all Methylsets so the number of features differs between datasets and an error message appears. In addition, I've different individuals in each Methylset (non conforming colnames) so I want to merge all individuals by the post filtering coincident probes. > > I would be very grateful if you can help me with this issue. > > Thanks in advance! > > Kind regards, > > Paula > > Post tags: minfi > > You may reply via email or visit C: support for EPIC methylation arrays in minfi
ADD REPLYlink written 9 months ago by Kasper Daniel Hansen6.3k

Hi Kasper,

I've solved the problem!

Many thanks for your quick answer!

 

Kind regards,

Paula

ADD REPLYlink written 9 months ago by paularl37730

Dear Kasper

Is the getNBeads function still active in minfi? I'm trying to process some EPIC arrays and establish how many probes are represented by less than 3 beads? Any advice appreciated.

All the best

Rachel

ADD REPLYlink written 4 months ago by r.clifford0
Yes it is. What version of minfi are you using? Best, Kasper On Thu, Jun 29, 2017 at 5:23 AM, r.clifford [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User r.clifford <https: support.bioconductor.org="" u="" 12781=""/> wrote Comment: > support for EPIC methylation arrays in minfi > <https: support.bioconductor.org="" p="" 79876="" #97575="">: > > Dear Kasper > > Is the getNBeads function still active in minfi? I'm trying to process > some EPIC arrays and establish how many probes are represented by less than > 3 beads? Any advice appreciated. > > All the best > > Rachel > > ------------------------------ > > Post tags: minfi > > You may reply via email or visit https://support.bioconductor. > org/p/79876/#97575 >
ADD REPLYlink written 4 months ago by Kasper Daniel Hansen6.3k

Hi Kasper. Thanks for your reply. I'm using version 1.20.2.

All the best

Rachel

ADD REPLYlink written 4 months ago by r.clifford0
The latest stable version is 1.22.1. You should update R and Bioconductor. On Fri, Jun 30, 2017 at 3:55 AM, r.clifford [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User r.clifford <https: support.bioconductor.org="" u="" 12781=""/> wrote Comment: > support for EPIC methylation arrays in minfi > <https: support.bioconductor.org="" p="" 79876="" #97623="">: > > Hi Kasper. Thanks for your reply. I'm using version 1.20.2. > > All the best > > Rachel > > ------------------------------ > > Post tags: minfi > > You may reply via email or visit https://support.bioconductor. > org/p/79876/#97623 >
ADD REPLYlink written 4 months ago by Kasper Daniel Hansen6.3k

Got it! Super, thank you.

Rachel

ADD REPLYlink written 4 months ago by r.clifford0
0
gravatar for line.heylen
15 months ago by
line.heylen0 wrote:

Hi Kasper,

I downloaded the new EPIC annotation package at Bioconductor (biocLite("IlluminaHumanMethylationEPICanno.ilm10b2.hg19")) but do not know how to extract the annotation from this data to a dataframe consisting of a column of CpGs with columns like p-values and T statistic; and I getting strange errors since (such as: lazy-load database '/Library/Frameworks/R.framework/Versions/3.3/Resources/library/minfi/help/minfi.rdb' is corrupt). 

Thank you for your help.

 

Best,

Line

 

ADD COMMENTlink written 15 months ago by line.heylen0
The errors sounds weird. Perhaps reinstall? Best, Kasper On Tue, Aug 9, 2016 at 1:49 PM, line.heylen [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User line.heylen <https: support.bioconductor.org="" u="" 10822=""/> wrote Answer: > support for EPIC methylation arrays in minfi > <https: support.bioconductor.org="" p="" 79876="" #85950="">: > > Hi Kasper, > > I downloaded the new EPIC annotation package at Bioconductor (biocLite(" > IlluminaHumanMethylationEPICanno.ilm10b2.hg19")) but do not know how to > extract the annotation from this data to a dataframe consisting of a > column of CpGs with columns like p-values and T statistic; and I getting > strange errors since (such as: lazy-load database '/Library/Frameworks/R. > framework/Versions/3.3/Resources/library/minfi/help/minfi.rdb' is > corrupt). > > Thank you for your help. > > > > Best, > > Line > > > > ------------------------------ > > Post tags: minfi > > You may reply via email or visit https://support.bioconductor. > org/p/79876/#85950 >
ADD REPLYlink written 15 months ago by Kasper Daniel Hansen6.3k
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