We are having some problems with the analysis of some EPIC methylation arrays (early access version) with minfi package. These arrays contains less cpgs than the current arrays so the annotation files are different.
When we tried to load the arrays with read.metharray function we get the error:
RGChannelSet (storageMode: lockedEnvironment)
assayData: 1032279 features, 1 samples
element names: Green, Red
An object of class 'AnnotatedDataFrame': none
We tried to create a new annotation object with the illumina bpm file and modify the read.metharray function but we obtained several incompatibility errors with the new annotation. Anyone knows how to create and attach the annotation required by minfi functions or how to deal with this kind of epic arrays?
Thank you very much.