diff --git a/R/ComBat.R b/R/ComBat.R index a2fbe96..187e6ec 100644 --- a/R/ComBat.R +++ b/R/ComBat.R @@ -59,7 +59,7 @@ ComBat <- function (dat, batch, mod = NULL, par.prior = TRUE, prior.plots = FALS if (!(ref.batch%in%levels(batch))) { stop("reference level ref.batch is not one of the levels of the batch variable") } - cat("Using batch =",ref.batch, "as a reference batch (this batch won't change)\n") + message("Using batch =",ref.batch, "as a reference batch (this batch won't change)") ref <- which(levels(as.factor(batch))==ref.batch) # find the reference batchmod[,ref] <- 1 } else { @@ -114,7 +114,7 @@ ComBat <- function (dat, batch, mod = NULL, par.prior = TRUE, prior.plots = FALS ## print(dat[1:2,]) ##Standardize Data across genes - cat('Standardizing Data across genes\n') + message('Standardizing Data across genes') if (!NAs){ B.hat <- solve(crossprod(design), tcrossprod(t(design), as.matrix(dat))) } else {