I have an EPIC beadchip methylation array that was stored in my lab, and remained unused past the expiration date. We wish to use it, together with newly bought ones, but apparently the DMAP files can only be downloaded from Illumina up to one year past the expiration date, and ours was not downloaded. It seems this policy was put in effect after we bought, but even though Illumina tech support told me they don't have the files anymore, which is a bit frustrating. So I was wondering, are all the DMAP files for different arrays unique, or are there different versions of DMAP files. Meaning, if I could get a DMAP file from another array, mainly if it was bought at a similar date, could I use that DMAP file in my array? Would that give me identical results, small differences in a few probes, or completely nonsensical results? I'm interested only in a few probes, so if somehow the results for those could be reliable, then it might be worth trying.
Infinium MethylationEPIC microarrays are based on the random beadchip technology. A BeadChip microarray consists of a silicon substrate with regularly interspaced micro-wells. Silicon micro-beads randomly self-assemble in the wells. Each bead is covered by hundreds of thousands of copies of the same 50-nucleotide long probe. During the manufacture, beads are pooled in equal ratio and then deposited on the array. As a result, the exact number of copies of each beadType is not controlled (varies from chip to chip). To assign the correspondence between microwells and bead types, decoding is required. This is done during manufacture via consecutive hybridizations with other sets of probes that target the address, a 23 nucleotide-long oligonucleotide handle that links the bead to the probe in the form of a DMAP file (Nakabayashi, 2017).
Thus, each DMAP file is specific to each microarray chip. It is standard practice to store methylation data as .IDAT files for the Green and the Red channel (that have already been decoded; e.g. bead at position x,y corresponds to bead "10600313"). I am not completely sure about this but I believe that in order to scan the microarray with iScan, you already need to provide a DMAP file. What is the current format of your data? If your data is in the .IDAT file, you do not need a DMAP file to analyze it (it has already been decoded). If your data is stored as images (.tiff) and the DMAP files cannot be retrieved, there will be no way to reliably link bead at position (x,y) to its bead type.
References
Nakabayashi K. Illumina HumanMethylation BeadChip for genome-wide DNA methylation profiling: advantages and limitations. In Handbook of Nutrition, Diet, and Epigenetics. Edited by Patel V, Preedy V. Cham: Springer International Publishing; 2017: 1-15
