Hi, I was wondering if anyone could confirm if the ChAMP package calls on plotMDS to display the 1000 most variable positions when running champ.load() and champ.norm(QCimages=T)?  If yes, then is plotMDS using the default gene.selection="pairwise" or the alternative ="common"?  Are the variable positions the Illumina CpG probes?  Is it possible to alter the argument top=1000? Thanks!