Hi Pan, I have 2 lumiBatch objects, both with controlData slots, filled in via addControlData2lumi. When I combine these 2 objects, the controlData was silently not combined. This is because my controlData slots had different numbers of rows. Could you please provide a warning within setMethod("combine", signature("LumiBatch","LumiBatch"), ...) if the nrow controlData don't match? if (nrow(x@controlData) > 0) { if (nrow(x@controlData) == nrow(y@controlData)) { controlData <- cbind(x@controlData, y@controlData) x@controlData <- as.data.frame(controlData) } else { warning("controlData slot not combined: different numbers of rows found") } } cheers, Mark ----------------------------------------------------- Mark Cowley, PhD Pancreatic Cancer Program | Peter Wills Bioinformatics Centre Garvan Institute of Medical Research, Sydney, Australia ----------------------------------------------------- [[alternative HTML version deleted]]