We are doing a methylation analysis for EPIC Illumina methylation beadchip data. We are comparing results using Partek (a commercial software) and minfi pipeline. We are finding some discrepancies between the result and on investigating deeper, we found was that starting number of probes were different, For Partek, which uses Illumina Manifest file it is 865818, whereas for the IlluminaHumanMethylationEPICanno.ilm10b4.hg19 is 865859. We double checked on the number of probes from the Illumina manifest files, and the number of probes is 865818.
Just checking whether there is any particular reason behind this discrepancy.
Hi,
We are doing a methylation analysis for EPIC Illumina methylation beadchip data. We are comparing results using Partek (a commercial software) and minfi pipeline. We are finding some discrepancies between the result and on investigating deeper, we found was that starting number of probes were different, For Partek, which uses Illumina Manifest file it is 865818, whereas for the IlluminaHumanMethylationEPICanno.ilm10b4.hg19 is 865859. We double checked on the number of probes from the Illumina manifest files, and the number of probes is 865818.
Just checking whether there is any particular reason behind this discrepancy.
Thanks, Surajit