I am analyzing a Methylation EPIC array data using ChAMP package. I observed that after apply champ.load() function, some extra probes are getting added to my actual probes list. Those probes were not present in the file imported by champ.import function and also not added when I perform champ.filter.
Since I want to use "SWAN" normalization in champ.norm() function I had to use champ.load(). When I applied champ.load(), the number of probes matching with manifest (EPIC.mainfest.hg19) are less. Ideally manifest file should have all the probes and coordinates for array data. But in my case I found, NOT all the probes present in myLoad$beta (which is a file after champ.load) or myNorm match with manifest and there are few hundred probes remain unassigned. The doubt is champ.load() seems to add some extra probes which are not present in my data. Here is my command:
> myLoad_2<-champ.load(directory = getwd(), > method="minfi", > methValue="B", > autoimpute=TRUE, > filterDetP=TRUE, > ProbeCutoff=0, > SampleCutoff=0.1, > detPcut=0.01, > filterBeads=TRUE, > beadCutoff=0.05, > filterNoCG=TRUE, > filterSNPs=TRUE, > population=NULL, > filterMultiHit=TRUE, > filterXY=TRUE, > force=FALSE, > arraytype="EPIC")
Number of probes remained after filtering: 705948 Number of filterd probes matched with manifest: 705762 Some extra probes I checked manually which were not overlapped with manifest: 186 Also I tried to check the origin and Some of these 186 probes overlapped with human.450K.manifest.csv file. How it is possible that when I give EPIC and probes were not present in my EPIC.manifest and also in my original data gets incorporated after champ.load().
I tried to look for solution but could not find anything.
I request you to please help me with the same.