Answers.Body: <p>We have been using SeSAMe, it works well for the most part. They have an enrichment tool called KnowYourCG. You can check it out their vignette: <a href="https://www.bioconductor.org/packages/release/bioc/vignettes/sesame/inst/doc/KYCG.html" rel="nofollow noreferrer">https://www.bioconductor.org/packages/release/bioc/vignettes/sesame/inst/doc/KYCG.html</a>.
  Note, SeSAMe and Minfi (and that suite of packages) have different data structures; However, for enrichment analysis, you only need probe IDs. Then you can use either curated databases from SeSAMe, or you can simply extract gene information, and run gprofiler2 as shown at the bottom part of the link I shared. Hope this helps.</p>
  
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Body: <p>Im analyzing methylation data from the new illumina's EPIC V2 array (900K).</p>
  <p>I would like to perform enrichment analysis on DMPs. In the past, I have always used missMethyl but since there are a lot of differences between EPIC V1 and EPIC V2 arrays I'm unsure if missMethyl can be used (Im afraid results might be biased)</p>
  <p>Does anyone know any enrichment tool already available for the EPIC V2 array or alternatives to missMethyl?</p>
  <p>Thanks</p>
  
Tags: <methylation><go-enrichment><epigenetics>
Title: Enrichment analysis of DMPs | new Ilumina EPIC V2 900K
ThreadText: # Enrichment analysis of DMPs | new Ilumina EPIC V2 900K
  
  (Asked by: username_0 on 2023-09-22)
  
  Im analyzing methylation data from the new illumina's EPIC V2 array (900K).
  
  I would like to perform enrichment analysis on DMPs. In the past, I have always used missMethyl but since there are a lot of differences between EPIC V1 and EPIC V2 arrays I'm unsure if missMethyl can be used (Im afraid results might be biased)
  
  Does anyone know any enrichment tool already available for the EPIC V2 array or alternatives to missMethyl?
  
  Thanks
  
  **Tags:** methylation, go-enrichment, epigenetics
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2024-05-20. Score: 1
  
  We have been using SeSAMe, it works well for the most part. They have an enrichment tool called KnowYourCG. You can check it out their vignette: <https://www.bioconductor.org/packages/release/bioc/vignettes/sesame/inst/doc/KYCG.html>.
  Note, SeSAMe and Minfi (and that suite of packages) have different data structures; However, for enrichment analysis, you only need probe IDs. Then you can use either curated databases from SeSAMe, or you can simply extract gene information, and run gprofiler2 as shown at the bottom part of the link I shared. Hope this helps.
  
  > **Comments:**
  > **username_2**: Welcome to the site and thanks for your answer  
  
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