Question: Infinium MethylationEPIC BeadChip probes with cross-hybridisation potential
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gravatar for AHW
18 months ago by
AHW40
India
AHW40 wrote:

I would like to get the latest list of probes with cross-hybridization potential Infinium MethylationEPIC BeadChip. I want to download the file and use it to remove the probes before performing any analysis. Can anybody help?

epic array • 517 views
ADD COMMENTlink modified 18 months ago by Charles Warden7.9k • written 18 months ago by AHW40
1
gravatar for Charles Warden
18 months ago by
Charles Warden7.9k
Duarte, CA
Charles Warden7.9k wrote:

While this may not be the best direct answer to your question, I believe Zhou et al. 2016 and Pidsley et al. 2016 can give you possible reasons for filtering probes on the EPIC array.

Other than that, highly overlapping probes may both have cross-hybridization potential. However, I would generally prefer to focus on regions with multiple (preferably, at least 4 probes) within a CpG Island. So, if the probes don't overlap (but are both in the same promoter for a gene), I think that can give you some additional confidence. Also, unless the cross-hybridization is a huge problem, using methylation thresholds (like average beta > 0.7 in one group and average beta < 0.3 in the other group) may help. Those are the sort of things that I have implemented in the COHCAP package.

ADD COMMENTlink modified 18 months ago • written 18 months ago by Charles Warden7.9k
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gravatar for Lemire
18 months ago by
Lemire590
Canada
Lemire590 wrote:

Check this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4909830/

ADD COMMENTlink written 18 months ago by Lemire590

Thank you for your comment. I already go the data from that paper and was wondering if it is up to date.

ADD REPLYlink written 18 months ago by AHW40
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