I am new to using Minfi, and I am running into some issues with the estimateCellCounts function. I have looked through some forums but can't seem to find anything that addresses the issue. I am processing around 180 samples from EPIC arrays and am getting almost all samples having a composition value of 0 for the granulocyte estimation. Some things I have thought to look into are converting my EPIC rgSet to a 450k rgSet, filtering down to less CpG probes (around 30,000), and using FlowSorted.Blood.EPIC. Each of these is either giving me the same results (0's for most of the granulocyte values) or is not running.
Have you seen this before? Any ideas what might be the issue with this?
Thanks for your help!