Question: query regarding using manifest and annotation in Minfi (EPIC Methylation array analysis)
gravatar for prasundutta87
3 months ago by
prasundutta87360 wrote:


I am analyzing some samples that were analyzed for methylation sites on an EPIC Methylation array (

I am trying to analyze it using the latest version of the Minfi package in R. I have a basic question regarding selecting the sample manifest file.

On checking the annotation using annotation() function for my object created using several IDAT files, I got this information-

   array                     annotation 
"IlluminaHumanMethylationEPIC"                 "ilm10b4.hg19"

I can clearly see that the annotation is "ilm10b4.hg19".

However, during pre-processing using preprocessRaw(), the function is automatically loading R package manifest namely IlluminaHumanMethylationEPICmanifest ( This is based on the array design for Illumina’s Human Methylation EPIC microarray and on the v1.0b2 version of the manifest file.

How can I make sure that the function chooses the correct manifest and its associated manifest? The R package of the correct annotation is also present in Bioconductor in this link- I have deleted the old manifest and downloaded and loaded the new manifest with new annotation. But, it hasn't worked. The preprocessRaw() function is still trying to choose the old manifest/annotation and failing.

methylation minfi epic array R • 162 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by prasundutta87360

Posting directly to Minfi GitHub page..

ADD REPLYlink written 3 months ago by prasundutta87360
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