Wrong terminology used on champ.load() output of ChAMP package?
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mariat • 0
@c1759fe5
Last seen 3 months ago
Belgium

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

ChAMPdata ChAMP • 305 views
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Probe means CpG probe in this context, each probe refers to one CpG site, they are almost synonym in the context of methylation array

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But isn't that a probe can have multiple CpG sites and thus we should not confuse these terms?

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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 dropXreactiveLoci function from the maxprobes package should be used to remove these probes from analysis.