The lumi package functions lumiB() and bgAdjust() mention the fact that control data can be used to background correct Illumina data. There is however no documentation regarding what the control data should contain, how it should be read it in, or exactly how it is used. I have summary probe profile data output from BeadStudio (not normalized or background corrected): Sample_Probe_Profile.txt I also have summary control probe data. This includes both positive and negative control probes: Control_Probe_Profile.txt How is it recommended that I read and use the control data, prior to using lumiT(method="vst")? A complete code example would be helpful. Gordon