I am analyzing some samples that were analyzed for methylation sites on an EPIC Methylation array (https://emea.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html).
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 (http://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylationEPICmanifest.html). 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-http://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylationEPICanno.ilm10b4.hg19.html. 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.