[BioC] High intensity probes might cause problems

Aileen Chefai aileen.chefai at helsinki.fi
Wed Nov 6 17:52:33 CET 2013


I am currently processing Infinium HumanMethylation450K BeadChips.  
While looking for all the necessary steps I read the paper 'A  
comprehensive overview of Infinium HumanMeththylation450 data  
processing' by Dedeurwaerder et al. There they say that one should  
exclude high intensity probes from the analysis as they might cause  
problems. Unfortunately, I could not really get how they define 'high  
intensity' - whether there is a certain cut-off in terms of a  
percentile or an actual value. Did anyone exclude these probes during  
preprocessing yet and could give a hint how to determine these 'high  
intensity probes' or tell me whether it is useful?

Thank, kind regards,

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