mwsill / illuminahumanmethylationepicv2manifest Goto Github PK

Hello,

I am able to get a methyl set and ratio set. But whenever I run mapToGenome the genomic ratio set or genomic methyl set are empty. I am using the new EPIC v2 manifest and IlluminaHumanMethylationEPICv2anno.20a1.hg38 annotation.

Also, the estimateCellCounts does not seem to work with the new array.

Thanks.

Hi, I used IlluminaHumanMethylationEPICv2manifest and minfi to get the Mset.

When trying to use Conumee, also the version from mwsill, I am running into this error when trying to create an annotation object:

using genome annotations from UCSC Loading required package: IlluminaHumanMethylationEPICv2anno.ilm10b4.hg19 Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'sort': cannot load annotation package IlluminaHumanMethylationEPICv2anno.ilm10b4.hg19

Can someone help me with this issue? Thanks!

Dear Martin,

Many thanks for providing this manifest. Are there any plans to create a separate annotation package for EPICv2? The reason I ask is that attempting to normalise with any other method in minfi returns an error, due to the lack of an accompanying IlluminaMethylationAnnotation object required by preprocessFunnorm() and other normalisation methods. Understanding the requirements and structure of the various minfi objects is a trial for me at the best of times, so thank you for getting the ball rolling.

Best,
Tim