"calcCPDs.MBnetwork.MBdataDE" <- function(x,data,contrasts=NULL) { isCompat <- compatObjects(x,data) if(is.null(contrasts)) fitLM <- eBayes(lmFit(data@M,design=data@design,weights=data@W,method=data@lmMethod),proportion=data@prop) else fitLM <- eBayes(contrasts.fit(lmFit(data@M,design=data@design,weights=data@W,method=data@lmMethod),contrasts),proportion=data@prop) x@Cpds <- calc.t.CPD(fitLM) return(x) }