I use minfi to import my EPIC data, and use pfilter from wateRmelon as the next step to remove probes and samples with high detection p-values and low bead counts etc.
I submit the RGset object to pfilter and get an Mset object back.
Mset.pf <- pfilter(RGset, perCount = 5, pnthresh = 0.01, perc = 1, pthresh = 1)
When I do this on my computer, the rownames of the Mset.pf object are of the form cg05575921, but if i do the same on another computer i get e.g. 1600101, which I think may be some address keys from illumina.
Does anyone know why i get these other numbers? Or how I can convert them to cg-numbers?
I can see that the Illumina Manifest file gets loaded...
Kind regards, Anne-Kristin
Ps my computer is not powerful enough to do the preprocessing on the full dataset, so this is why I need it to work on another computer...