I have 450k and EPIC data that I would like to process at the same time and analyse the whole matrix at once. I am using minfi package, which contains the combineArray() function that is intended to merge 450k and EPIC data. However, when using it, it automatically drops all the probes in the EPIC array that are not in the 450k array, which is totally an unwanted behaviour since I lose half of the probes of the EPIC array. Does anybody know an alternative solution to analyze both platforms together?

minfi version 1.30.0

Many thanks in advance,

If you don't drop the EPIC-only probes, your matrix will have this great huge block of probes that are NA for all the samples that were run on the 450K arrays, for which any analysis will only use the EPIC data. So it doesn't make any sense to do anything but drop the EPIC-only probes, because you can just analyze those separately anyway.