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Hello everyone, I am using ChAMP package for an analysis and I was wondering if some terminology is wrongly used at some point of the output of the champ.load() function, as it has caused me some confusion. I am referring to this outputted block of text, which is printed after the filtering results:
[ Section 2: Filtering Done ]
All filterings are Done, now you have 490066 probes and 2 samples.
[<<<<< ChAMP.FILTER END >>>>>>]
[===========================]
[You may want to process champ.QC() next.]
Since the filtering has been done on the CpG level, the right way wouldn't be to say :
"All filterings are Done, now you have 490066 CpGs and 2 samples."
? Thank you in advance, Maria
Probe means CpG probe in this context, each probe refers to one CpG site, they are almost synonym in the context of methylation array
But isn't that a probe can have multiple CpG sites and thus we should not confuse these terms?
One probe can capture only one CpG locus. There are particular cases where probes are "cross-reactive", meaning that some probes are not specific to only one CpG locus (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3592906/) and this is why some great tools such as the
dropXreactiveLocifunction from themaxprobespackage should be used to remove these probes from analysis.