[BioC] lumi, Illumina Methylation 450k, and robust methylation calls

Ina Hoeschele inah at vbi.vt.edu
Tue Jun 14 00:05:16 CEST 2011

I have recently started to use the lumi package to analyse some
Illumina Human Methylation 450k data, and I have run into some
problems which seem to revolve around division by zero in the
gammaFitEM() function. I have adjusted the colour balance and quantile
normalised as suggested in the vignette

Hi Pan and Tim (et al),
   this is in regard to an earlier email from Tim - is the colour balance adjustment performed for ALL probes or only for probes with Infinium I assay? Is the quantile normalization done for both Inf I and II together (rather than separately) in the current (development) version of lumi? I would be reluctant to do it that way, and I apologize if this is described somewhere and I misssed this informaiton.
Thanks, Ina

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