Hi all,

I have EPIC array data analysed, but colleagues are concerned about annotation which is massively incomplete: 56% of probes do not have UCSC 'relation to CpG island' data, and 25% no gene annotated. This seems crazy to me, but is confirmed by Illumina. They say a lot of users go and annotate from public resources. 

I presume others have come across this? Any chance anyone has a full(er) annotation? Or even ideas on where to source/create?

Thanks, Bruce.
The annotation that comes with [Minfi][1]'s workflow is generally pretty complete...but as with anything, it has gaps. The manifest that Minfi uses is [here][2]. Check out the annotation there and see if it's as incomplete as Illumina have suggested to you. 


  [1]: http://bioconductor.org/packages/release/bioc/html/minfi.html
  [2]: https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylationEPICmanifest.html